MOSAICS for paired end data
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SR
Aug 15, 2012, 9:22:51 PM8/15/12
to mosaics_u...@googlegroups.com
Hello,
I would like to try MOSAICS on my dataset. I have paired-end ChipSeq data. How can I use them? How should I change the scripts to take this into account?
Thank you!
Regards,
Sigrid
I would like to try MOSAICS on my dataset. I have paired-end ChipSeq data. How can I use them? How should I change the scripts to take this into account?
Thank you!
Regards,
Sigrid
Dongjun Chung
Aug 15, 2012, 11:04:22 PM8/15/12
to mosaics_u...@googlegroups.com
Hi Sigrid,
Thanks for your interest in our mosaics package.
When constructBins() function in the current version of mosaics package in bioconductor processes aligned read files, it assumes SET ChIP-seq data. In order to handle PET ChIP-seq data, I wrote a perl script to process PET aligned read files to bin-level files. Currently, it supports eland result and SAM file formats. If your file is in one of these file formats, I can send you this perl script and you can just utilize this perl script. Otherwise, I can modify the perl script so that it can handle your file format. Please just let me know which is your case.
Briefly, for SET data, mosaics extends each read to its 3' end by average fragment length. For PET data, each paired reads contributes to the positions that are located between two ends of the paired reads.
I plan to incorporate this perl script into the mosaics package soon. So, in the next version of mosaics package, constructBins() function will be able to process PET aligned read files as well.
Thanks,
Dongjun
Thanks for your interest in our mosaics package.
When constructBins() function in the current version of mosaics package in bioconductor processes aligned read files, it assumes SET ChIP-seq data. In order to handle PET ChIP-seq data, I wrote a perl script to process PET aligned read files to bin-level files. Currently, it supports eland result and SAM file formats. If your file is in one of these file formats, I can send you this perl script and you can just utilize this perl script. Otherwise, I can modify the perl script so that it can handle your file format. Please just let me know which is your case.
Briefly, for SET data, mosaics extends each read to its 3' end by average fragment length. For PET data, each paired reads contributes to the positions that are located between two ends of the paired reads.
I plan to incorporate this perl script into the mosaics package soon. So, in the next version of mosaics package, constructBins() function will be able to process PET aligned read files as well.
Thanks,
Dongjun
Sigrid Rouam
Aug 15, 2012, 11:57:21 PM8/15/12
to mosaics_u...@googlegroups.com
Hi Dongjun,
thank you very much for your reply.
Our data consists of PET SAM files aligned using BWA.
I would be grateful if you could send me your scripts.
Regards,
Sigrid
thank you very much for your reply.
Our data consists of PET SAM files aligned using BWA.
I would be grateful if you could send me your scripts.
Regards,
Sigrid
2012/8/16 Dongjun Chung <dongju...@gmail.com>
Dongjun Chung
Aug 15, 2012, 11:59:48 PM8/15/12
to mosaics_u...@googlegroups.com
Hi Sigrid,
This sounds great. Then, I can think that you can use the script. Just to make sure, can you provide the first few lines of your file?
Thanks,
Dongjun
This sounds great. Then, I can think that you can use the script. Just to make sure, can you provide the first few lines of your file?
Thanks,
Dongjun
Sigrid Rouam
Aug 17, 2012, 3:00:23 AM8/17/12
to mosaics_u...@googlegroups.com
Hi Dongjun,
we are having problems on our work server for the moment. I am not able to retrieve the SAM files. I hope the IT department will fix this issue soon, so that I can send you the first lines of my data!
Thank you.
we are having problems on our work server for the moment. I am not able to retrieve the SAM files. I hope the IT department will fix this issue soon, so that I can send you the first lines of my data!
Thank you.
Sigrid Rouam
Aug 17, 2012, 5:58:14 AM8/17/12
to mosaics_u...@googlegroups.com
Hello Dongjun,
here is the first few lines of my SAM file.
I would be glad to be able to try your normalization on it!
Thank you.
Regards,
Sigrid
@SQ SN:1 LN:249250621
@SQ SN:2 LN:243199373
@SQ SN:3 LN:198022430
@SQ SN:4 LN:191154276
@SQ SN:5 LN:180915260
@SQ SN:6 LN:171115067
@SQ SN:7 LN:159138663
@SQ SN:8 LN:146364022
@SQ SN:9 LN:141213431
@SQ SN:10 LN:135534747
@SQ SN:11 LN:135006516
@SQ SN:12 LN:133851895
@SQ SN:13 LN:115169878
@SQ SN:14 LN:107349540
@SQ SN:15 LN:102531392
@SQ SN:16 LN:90354753
@SQ SN:17 LN:81195210
@SQ SN:18 LN:78077248
@SQ SN:19 LN:59128983
@SQ SN:20 LN:63025520
@SQ SN:21 LN:48129895
@SQ SN:22 LN:51304566
@SQ SN:X LN:155270560
@SQ SN:Y LN:59373566
@SQ SN:MT LN:16569
@SQ SN:GL000207.1 LN:4262
@SQ SN:GL000226.1 LN:15008
@SQ SN:GL000229.1 LN:19913
@SQ SN:GL000231.1 LN:27386
@SQ SN:GL000210.1 LN:27682
@SQ SN:GL000239.1 LN:33824
@SQ SN:GL000235.1 LN:34474
@SQ SN:GL000201.1 LN:36148
@SQ SN:GL000247.1 LN:36422
@SQ SN:GL000245.1 LN:36651
@SQ SN:GL000197.1 LN:37175
@SQ SN:GL000203.1 LN:37498
@SQ SN:GL000246.1 LN:38154
@SQ SN:GL000249.1 LN:38502
@SQ SN:GL000196.1 LN:38914
@SQ SN:GL000248.1 LN:39786
@SQ SN:GL000244.1 LN:39929
@SQ SN:GL000238.1 LN:39939
@SQ SN:GL000202.1 LN:40103
@SQ SN:GL000234.1 LN:40531
@SQ SN:GL000232.1 LN:40652
@SQ SN:GL000206.1 LN:41001
@SQ SN:GL000240.1 LN:41933
@SQ SN:GL000236.1 LN:41934
@SQ SN:GL000241.1 LN:42152
@SQ SN:GL000243.1 LN:43341
@SQ SN:GL000242.1 LN:43523
@SQ SN:GL000230.1 LN:43691
@SQ SN:GL000237.1 LN:45867
@SQ SN:GL000233.1 LN:45941
@SQ SN:GL000204.1 LN:81310
@SQ SN:GL000198.1 LN:90085
@SQ SN:GL000208.1 LN:92689
@SQ SN:GL000191.1 LN:106433
@SQ SN:GL000227.1 LN:128374
@SQ SN:GL000228.1 LN:129120
@SQ SN:GL000214.1 LN:137718
@SQ SN:GL000221.1 LN:155397
@SQ SN:GL000209.1 LN:159169
@SQ SN:GL000218.1 LN:161147
@SQ SN:GL000220.1 LN:161802
@SQ SN:GL000213.1 LN:164239
@SQ SN:GL000211.1 LN:166566
@SQ SN:GL000199.1 LN:169874
@SQ SN:GL000217.1 LN:172149
@SQ SN:GL000216.1 LN:172294
@SQ SN:GL000215.1 LN:172545
@SQ SN:GL000205.1 LN:174588
@SQ SN:GL000219.1 LN:179198
@SQ SN:GL000224.1 LN:179693
@SQ SN:GL000223.1 LN:180455
@SQ SN:GL000195.1 LN:182896
@SQ SN:GL000212.1 LN:186858
@SQ SN:GL000222.1 LN:186861
@SQ SN:GL000200.1 LN:187035
@SQ SN:GL000193.1 LN:189789
@SQ SN:GL000194.1 LN:191469
@SQ SN:GL000225.1 LN:211173
@SQ SN:GL000192.1 LN:547496
HWI-ST740_0001:1:1101:1222:2116#0 83 5 159866484 60 92M = 159866412 -164 AGAGCGTGGAGCTGACCCTCATGTTAGTGTGATAGATTTCTAGTCACGTGTACCCACCATGAGTACAGTCAGATGCTTTAAAATTTTAGTTT GGHGEHHGFGFFGGCGG?D
CDF?FE;FHHHHHFHHHHGBGGGFBDDDDHHECHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHFHHHHH XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:92
HWI-ST740_0001:1:1101:1222:2116#0 163 5 159866412 60 88M = 159866484 164 CCCGTTAGACTCTTCCTGAGGTCCCCGGAGTGGCACAGGGGGTTGTGGTGGAGAGTGAAGCGAAGAAGTCACAGAGCGTGGAGCTGAC HHHHHHHHHHHHHHHHHHH
HHHHHHGGGFGDFHHGHHHHHHHDHHCFGAFGEEEECGFEGHHHHHEHHCFHHHHHHEHBHHFGBEHHB XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1095:2131#0 99 19 41945325 60 92M = 41945428 191 CATGNTTTTGAGTTTTCTGTAAAAATTCGTCAATCTCCCACTAACTTTCCTTACATTCATCCTTCGGTCTTCTAAGACCAAATCCCACATCC CACC%DDDDDHHHHHHHHH
HHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHFHHHHHHEHHBGFF;GGGGGGHGHGHHEGHHH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4C87
HWI-ST740_0001:1:1101:1095:2131#0 147 19 41945428 60 88M = 41945325 -191 CTTCCAAGCTCTCTTATCCTACAGGCCCCCCCCTTGCCTGTCCATTAGCTCCTTGTGTCATCCCTCCCTCTGATTGGTTAGTCGCGTC ?D=D@AA>CAD?DC>B>D@
>@>;EEEEED)DDDGGCGEHHBHHHHHHHHBHHHHHHHGHHFHHHFHHHHHHHHHHHHHHHHHHHHHHH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:29A58
HWI-ST740_0001:1:1101:1195:2138#0 99 16 23169966 60 92M = 23170207 329 CCCTATGTTAAGCCCCATGCTTAAGCTTACCCAGCTTTTGCTGCATCTGATGCCTCCAATTCCCGACTATGTTAGTTGGGGCTGTGTGATGG HGHHHHHHHHHHEHHHHHH
HHGHHHHHHGFHHHHGHHHHHHHHHFHHHGHFHHEHHHFEHHFHFHHHHHHGFEHHFGGFGHHHHDFEGGGGG XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:92
HWI-ST740_0001:1:1101:1195:2138#0 147 16 23170207 60 88M = 23169966 -329 TCAGCTGCCAGTGTGGTTAGAATAAAAGCAGGCCGCAGAACGTGGAAGGACTTGACTTGCTGAGTCTTCCGGCCTTCATCTTTCTCCC <>4>HHGFHHHHHHHHHHG
HHHHHHHFHHHHHHIGIHGFDHFHHHHHFHEHHEHEHHHEHFHHHHHHHHHHFHHFEHHHHHHHHHHHH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:36C51
HWI-ST740_0001:1:1101:1090:2159#0 83 14 102457791 60 92M = 102457573 -310 AAACTCTGTCTTAAAAAAATTTTTTTTATTGAAAAATAGATTGCTGAGTAGAAATGAAACCTTTCTTTCACAGAATGTCGTTCATGANCTAA CFCGGDGHHEHHFFFFEBA
??CBEA6ACDFHEGHHHHFCHEFFFFGGHHEHHEFDDE7EGGGEAFDGHFFHGHDHHEFGGFGAAA@A%?<?< XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:87G4
HWI-ST740_0001:1:1101:1090:2159#0 163 14 102457573 60 88M = 102457791 310 GGCTGAAGCGGGTGGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGACCAACATGCTGAAACCCGTCTCTACTAAAAATATATAAT DCACABEECDFDBFA?BEC
EB>FFDE8D?FE;CAEEF<DEF<DCA9AAA;DEDDEHHBHHDEBEEFH?BCAADAD?BAACFDEB@D:< XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:43A44
HWI-ST740_0001:1:1101:1221:2162#0 83 9 116274509 60 92M = 116274458 -143 TCTTGAGACTGAGGATGGTGCTTTAAACAAAGGGTCCAGGGCCTGGCAGCACACATCCCTCTGGGACTGATATGTAGGGCCAGATCAGACAA HDGHHHBHHGHFHGHEHHB
FGGGDHGHHHHHHFHHHHHHHHHHHHHGHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:92
HWI-ST740_0001:1:1101:1221:2162#0 163 9 116274458 60 88M = 116274509 143 GAAGTCAGTGATCAAGCTCGGGTGTCTTATCCAACTCAAATTCAGTGATGATCTTGAGACTGAGGATGGTGCTTTAAACAAAGGGTCC HHHHHHHHHHHHHHHHHHH
HHHBHFHHHHHFHHHHHHHHHHHHHHFHHFHHHHHHHHHFHHHHFHHHHHHHHHHHDBGHFHHCFH?FG XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1125:2168#0 99 12 96944707 60 92M = 96944869 250 AGTTNGAACCTACAAAAGATTATATCCTAGGAAAAGGTAGACTAGAAAAAAACTCTGGCCTGGGTATGGTGGCTCACGCCTTTTATCCTAGC BCAC%GGDGDHHHGHHHHH
HHHHHHHHHHHHHHHHHHEHHGHHHFEHHGHHHHEHHHHFHHHHHEEFCFDEGADDFFFFFBIFEF::C:@B< XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4A87
HWI-ST740_0001:1:1101:1125:2168#0 147 12 96944869 60 88M = 96944707 -250 AAACCATGACTCTGCAAAAAAAATACAAAAATTAGCTGGGTGTGATGACATGTGCCTGTAGTCCTAGCTACTTGGGAGGATCGCCTGA HHHHHGHHEGGGGFEHHHH
GHHHHHHHHHHHHHHHHHHHGHHHHHFHHHHHHHFHHHFHHHHHHFHHHHHHHHHHHHHHHGHFHHHHH XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1155:2173#0 99 10 5727936 60 92M = 5727949 101 GTCTNCAGTGTTCCCTGAATAAAACTAGGGGTGAGCCTGGCGGTAATCCTGCCTAGGAGGTTTATAGCAAAGCAGTGTCCCCTAACGGTGCA CBCC%DDDDDHHHHHHHGFHHHHHHHGHHHHEHHH
EHHHHDHHDFHFHHHHHHFHHHHHHDHFEFFGECFCFFFEHGFHHHHHHGGHHFHGH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4A87
HWI-ST740_0001:1:1101:1155:2173#0 147 10 5727949 60 88M = 5727936 -101 CCTGAATAAAACTAGGGGTGAGCCTGGCGGTAATCCTGCCTAGGAGGTTTATAGCAAAGCAGTGTCCCCTAACGGTGCAAGAATACCC EE>EHFHFED9EEDHHHAFFHEHFFFGHD9GGFEG
GDEHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHGDGHI XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1099:2182#0 99 2 38974888 60 92M = 38975118 318 GTATNATCCAATCTGAAGCCAGAAAAGTTTATAGCAACATGCCTACCCAGAGTGTTGAGTAGAACTGTATTGCTTGGGACCCTTGTCTACCA C?BC%DDDDDHHHHHHHHH
HHHGHHHHEHHHHHGHHHHHHHFHHHHHHHHFG?GEHHFHFFHFDHFHFBFHHHFFHHHHHHHHHHHHEHHEH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4C87
HWI-ST740_0001:1:1101:1099:2182#0 147 2 38975118 60 88M = 38974888 -318 TGTCCTTAAGACACTCTACTGATAAGATGTGAACAATCCAAACACAAGTAAGGAAAAAAAGTGTTACATACTGGAAATACCTCGATCC HHHHHFHHGHEHCHGHHHH
HHHHHHHHEHHHHHHHHHHFHHHHFHHHHHHHHHHHFHHHHFHFIGFGFFFHHHHHHHHDHHHHHHHHH XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1067:2205#0 83 8 96090111 60 12S80M = 96089991 -200 ATGAGCAAAAGGCAAGCCAGTCTAGGTGCATGGCCAGCCCCCCGAGATGGAGCTCATGGTGAGGGACCAGCCAAGTCAATCACATCTNCCTT %%%%%%%%%%%%%@;7@C<
BBCDCFEECDC5CCFCC4HHHHHDFDG?FHCFEEEEBFDCDDBGFF@FFHHHFHHHHHHHHHFDCDCD%AAAB XC:i:80 XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:75G4
HWI-ST740_0001:1:1101:1067:2205#0 163 8 96089991 60 88M = 96090111 200 TTGTAAAGGTCATGAGAAGTGCCTGTCCCTCCAAGGGTGCAAGGGTGACCAGAAGCAAGCTCTTAGGCATGGGTGGGCTTGCTGTGGA HHHHHHHHHHHHHHHHHEH
FHHHHHFHHHHHHHHHFHDHHFEHHHBFEFFGGGIGHHHHHHGHHHHEHHHHHHDHDGGEEHHBHCGFF XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1092:2208#0 99 16 23963265 60 92M = 23963410 233 GGTGNTGACCTGTTTGTCTCCCTGGCTGTCAGACTGTGAGAAACTTGAGGGCAGGGGCTGTACTTTATTCTTCTCTGTCTCTCTAGGGACTA >86;%8>===FHFHHHECH
FFEE?FFBFEEFHFEFEEHHH?DCD+FACBDF<EFECFE9C9=C?CD5C<0C<CC:6@0><DDDE<FCBDFCB XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4G87
HWI-ST740_0001:1:1101:1092:2208#0 147 16 23963410 60 88M = 23963265 -233 ACGTGGTATAAAACAGGTCTTGTGACTGAATGAGGGAATGAATGAAAAAGCCCTGTCCTGCCCTCCCTGCAGAGATGGGGTCTGCTGC @EAD>C?E<?DAADC==:H
EDDFDGFEFDCC9D@;@B75BDFBC@DFD?B?FFBFFFFDDDDD9D@FBHHBHEFGACGC@BDEFFDFG XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1177:2226#0 99 1 182615131 60 92M = 182615381 338 TTTGCAAGCTGTATCTTTCTTAATGGCAGTTCCACTTCAGAAGTCATGAAGAACATCACCCAAGACTCTTTCTGGAAATGTAAGGTTAGGGT HHHHHHHHHHHHHHHHHHH
HHHGHHHHHG9DADADCFDBFEFE?FHHFBHFCHCHHEHFCD<DFDCAFEEGEBF>CBGEGDDFFE@E7?E@3 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:92
HWI-ST740_0001:1:1101:1177:2226#0 147 1 182615381 60 88M = 182615131 -338 TCTCTCCTAAGCTGTGAGATCCCAGTGAGCAGAGCTGGCCACTACAAATCACAGAGTTGAGCCTAAGTCTTTCAGCTATTCCTCCCAG <=7D@D?DE:6EBG<BDF@
<DD69EEEE<CEEDBAIFGGGCGBEGFGFEGEGFHHHHFHHHHHGGGGBGHHFHHFHHHHEGHHHHHHH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:63C24
HWI-ST740_0001:1:1101:1066:2233#0 99 11 122934086 60 92M = 122934250 252 ACGANAGACCATACCGACGCTTTGAAAACGTGACTGAGCTGGTGCACAAAACAATGGTGCCTAGAATTTTGAATTGTGCAATGTTGTGCATG BABA%DDDDDGHHHHHHHH
HHHHHHHFHHHHHHHHHHHHHHHEHHCHHFHEHHHHHHEHFCEEGDFFFFHHFHHHHHHHHHHHEHHFHHFHH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4C87
HWI-ST740_0001:1:1101:1066:2233#0 147 11 122934250 60 88M = 122934086 -252 AAGCAGGCGAGGTAGCTGTTATTCCTATTTAGTAGATAAATAGGCACCGATGGGGGAAAAGATTTTTTAAGGCTACACCAAAAGAACT HHHHHHHGDHHHHHHHGGH
FHHHGHHHHDBHHHHHHHHHH@HHHHFHHHHHHHFHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHH XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
here is the first few lines of my SAM file.
I would be glad to be able to try your normalization on it!
Thank you.
Regards,
Sigrid
@SQ SN:1 LN:249250621
@SQ SN:2 LN:243199373
@SQ SN:3 LN:198022430
@SQ SN:4 LN:191154276
@SQ SN:5 LN:180915260
@SQ SN:6 LN:171115067
@SQ SN:7 LN:159138663
@SQ SN:8 LN:146364022
@SQ SN:9 LN:141213431
@SQ SN:10 LN:135534747
@SQ SN:11 LN:135006516
@SQ SN:12 LN:133851895
@SQ SN:13 LN:115169878
@SQ SN:14 LN:107349540
@SQ SN:15 LN:102531392
@SQ SN:16 LN:90354753
@SQ SN:17 LN:81195210
@SQ SN:18 LN:78077248
@SQ SN:19 LN:59128983
@SQ SN:20 LN:63025520
@SQ SN:21 LN:48129895
@SQ SN:22 LN:51304566
@SQ SN:X LN:155270560
@SQ SN:Y LN:59373566
@SQ SN:MT LN:16569
@SQ SN:GL000207.1 LN:4262
@SQ SN:GL000226.1 LN:15008
@SQ SN:GL000229.1 LN:19913
@SQ SN:GL000231.1 LN:27386
@SQ SN:GL000210.1 LN:27682
@SQ SN:GL000239.1 LN:33824
@SQ SN:GL000235.1 LN:34474
@SQ SN:GL000201.1 LN:36148
@SQ SN:GL000247.1 LN:36422
@SQ SN:GL000245.1 LN:36651
@SQ SN:GL000197.1 LN:37175
@SQ SN:GL000203.1 LN:37498
@SQ SN:GL000246.1 LN:38154
@SQ SN:GL000249.1 LN:38502
@SQ SN:GL000196.1 LN:38914
@SQ SN:GL000248.1 LN:39786
@SQ SN:GL000244.1 LN:39929
@SQ SN:GL000238.1 LN:39939
@SQ SN:GL000202.1 LN:40103
@SQ SN:GL000234.1 LN:40531
@SQ SN:GL000232.1 LN:40652
@SQ SN:GL000206.1 LN:41001
@SQ SN:GL000240.1 LN:41933
@SQ SN:GL000236.1 LN:41934
@SQ SN:GL000241.1 LN:42152
@SQ SN:GL000243.1 LN:43341
@SQ SN:GL000242.1 LN:43523
@SQ SN:GL000230.1 LN:43691
@SQ SN:GL000237.1 LN:45867
@SQ SN:GL000233.1 LN:45941
@SQ SN:GL000204.1 LN:81310
@SQ SN:GL000198.1 LN:90085
@SQ SN:GL000208.1 LN:92689
@SQ SN:GL000191.1 LN:106433
@SQ SN:GL000227.1 LN:128374
@SQ SN:GL000228.1 LN:129120
@SQ SN:GL000214.1 LN:137718
@SQ SN:GL000221.1 LN:155397
@SQ SN:GL000209.1 LN:159169
@SQ SN:GL000218.1 LN:161147
@SQ SN:GL000220.1 LN:161802
@SQ SN:GL000213.1 LN:164239
@SQ SN:GL000211.1 LN:166566
@SQ SN:GL000199.1 LN:169874
@SQ SN:GL000217.1 LN:172149
@SQ SN:GL000216.1 LN:172294
@SQ SN:GL000215.1 LN:172545
@SQ SN:GL000205.1 LN:174588
@SQ SN:GL000219.1 LN:179198
@SQ SN:GL000224.1 LN:179693
@SQ SN:GL000223.1 LN:180455
@SQ SN:GL000195.1 LN:182896
@SQ SN:GL000212.1 LN:186858
@SQ SN:GL000222.1 LN:186861
@SQ SN:GL000200.1 LN:187035
@SQ SN:GL000193.1 LN:189789
@SQ SN:GL000194.1 LN:191469
@SQ SN:GL000225.1 LN:211173
@SQ SN:GL000192.1 LN:547496
HWI-ST740_0001:1:1101:1222:2116#0 83 5 159866484 60 92M = 159866412 -164 AGAGCGTGGAGCTGACCCTCATGTTAGTGTGATAGATTTCTAGTCACGTGTACCCACCATGAGTACAGTCAGATGCTTTAAAATTTTAGTTT GGHGEHHGFGFFGGCGG?D
CDF?FE;FHHHHHFHHHHGBGGGFBDDDDHHECHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHFHHHHH XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:92
HWI-ST740_0001:1:1101:1222:2116#0 163 5 159866412 60 88M = 159866484 164 CCCGTTAGACTCTTCCTGAGGTCCCCGGAGTGGCACAGGGGGTTGTGGTGGAGAGTGAAGCGAAGAAGTCACAGAGCGTGGAGCTGAC HHHHHHHHHHHHHHHHHHH
HHHHHHGGGFGDFHHGHHHHHHHDHHCFGAFGEEEECGFEGHHHHHEHHCFHHHHHHEHBHHFGBEHHB XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1095:2131#0 99 19 41945325 60 92M = 41945428 191 CATGNTTTTGAGTTTTCTGTAAAAATTCGTCAATCTCCCACTAACTTTCCTTACATTCATCCTTCGGTCTTCTAAGACCAAATCCCACATCC CACC%DDDDDHHHHHHHHH
HHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHFHFHHHHHHEHHBGFF;GGGGGGHGHGHHEGHHH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4C87
HWI-ST740_0001:1:1101:1095:2131#0 147 19 41945428 60 88M = 41945325 -191 CTTCCAAGCTCTCTTATCCTACAGGCCCCCCCCTTGCCTGTCCATTAGCTCCTTGTGTCATCCCTCCCTCTGATTGGTTAGTCGCGTC ?D=D@AA>CAD?DC>B>D@
>@>;EEEEED)DDDGGCGEHHBHHHHHHHHBHHHHHHHGHHFHHHFHHHHHHHHHHHHHHHHHHHHHHH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:29A58
HWI-ST740_0001:1:1101:1195:2138#0 99 16 23169966 60 92M = 23170207 329 CCCTATGTTAAGCCCCATGCTTAAGCTTACCCAGCTTTTGCTGCATCTGATGCCTCCAATTCCCGACTATGTTAGTTGGGGCTGTGTGATGG HGHHHHHHHHHHEHHHHHH
HHGHHHHHHGFHHHHGHHHHHHHHHFHHHGHFHHEHHHFEHHFHFHHHHHHGFEHHFGGFGHHHHDFEGGGGG XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:92
HWI-ST740_0001:1:1101:1195:2138#0 147 16 23170207 60 88M = 23169966 -329 TCAGCTGCCAGTGTGGTTAGAATAAAAGCAGGCCGCAGAACGTGGAAGGACTTGACTTGCTGAGTCTTCCGGCCTTCATCTTTCTCCC <>4>HHGFHHHHHHHHHHG
HHHHHHHFHHHHHHIGIHGFDHFHHHHHFHEHHEHEHHHEHFHHHHHHHHHHFHHFEHHHHHHHHHHHH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:36C51
HWI-ST740_0001:1:1101:1090:2159#0 83 14 102457791 60 92M = 102457573 -310 AAACTCTGTCTTAAAAAAATTTTTTTTATTGAAAAATAGATTGCTGAGTAGAAATGAAACCTTTCTTTCACAGAATGTCGTTCATGANCTAA CFCGGDGHHEHHFFFFEBA
??CBEA6ACDFHEGHHHHFCHEFFFFGGHHEHHEFDDE7EGGGEAFDGHFFHGHDHHEFGGFGAAA@A%?<?< XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:87G4
HWI-ST740_0001:1:1101:1090:2159#0 163 14 102457573 60 88M = 102457791 310 GGCTGAAGCGGGTGGATCACCTGAGGTCAGGAGTTTGAGACCAGCCTGACCAACATGCTGAAACCCGTCTCTACTAAAAATATATAAT DCACABEECDFDBFA?BEC
EB>FFDE8D?FE;CAEEF<DEF<DCA9AAA;DEDDEHHBHHDEBEEFH?BCAADAD?BAACFDEB@D:< XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:43A44
HWI-ST740_0001:1:1101:1221:2162#0 83 9 116274509 60 92M = 116274458 -143 TCTTGAGACTGAGGATGGTGCTTTAAACAAAGGGTCCAGGGCCTGGCAGCACACATCCCTCTGGGACTGATATGTAGGGCCAGATCAGACAA HDGHHHBHHGHFHGHEHHB
FGGGDHGHHHHHHFHHHHHHHHHHHHHGHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:92
HWI-ST740_0001:1:1101:1221:2162#0 163 9 116274458 60 88M = 116274509 143 GAAGTCAGTGATCAAGCTCGGGTGTCTTATCCAACTCAAATTCAGTGATGATCTTGAGACTGAGGATGGTGCTTTAAACAAAGGGTCC HHHHHHHHHHHHHHHHHHH
HHHBHFHHHHHFHHHHHHHHHHHHHHFHHFHHHHHHHHHFHHHHFHHHHHHHHHHHDBGHFHHCFH?FG XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1125:2168#0 99 12 96944707 60 92M = 96944869 250 AGTTNGAACCTACAAAAGATTATATCCTAGGAAAAGGTAGACTAGAAAAAAACTCTGGCCTGGGTATGGTGGCTCACGCCTTTTATCCTAGC BCAC%GGDGDHHHGHHHHH
HHHHHHHHHHHHHHHHHHEHHGHHHFEHHGHHHHEHHHHFHHHHHEEFCFDEGADDFFFFFBIFEF::C:@B< XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4A87
HWI-ST740_0001:1:1101:1125:2168#0 147 12 96944869 60 88M = 96944707 -250 AAACCATGACTCTGCAAAAAAAATACAAAAATTAGCTGGGTGTGATGACATGTGCCTGTAGTCCTAGCTACTTGGGAGGATCGCCTGA HHHHHGHHEGGGGFEHHHH
GHHHHHHHHHHHHHHHHHHHGHHHHHFHHHHHHHFHHHFHHHHHHFHHHHHHHHHHHHHHHGHFHHHHH XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1155:2173#0 99 10 5727936 60 92M = 5727949 101 GTCTNCAGTGTTCCCTGAATAAAACTAGGGGTGAGCCTGGCGGTAATCCTGCCTAGGAGGTTTATAGCAAAGCAGTGTCCCCTAACGGTGCA CBCC%DDDDDHHHHHHHGFHHHHHHHGHHHHEHHH
EHHHHDHHDFHFHHHHHHFHHHHHHDHFEFFGECFCFFFEHGFHHHHHHGGHHFHGH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4A87
HWI-ST740_0001:1:1101:1155:2173#0 147 10 5727949 60 88M = 5727936 -101 CCTGAATAAAACTAGGGGTGAGCCTGGCGGTAATCCTGCCTAGGAGGTTTATAGCAAAGCAGTGTCCCCTAACGGTGCAAGAATACCC EE>EHFHFED9EEDHHHAFFHEHFFFGHD9GGFEG
GDEHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHGDGHI XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1099:2182#0 99 2 38974888 60 92M = 38975118 318 GTATNATCCAATCTGAAGCCAGAAAAGTTTATAGCAACATGCCTACCCAGAGTGTTGAGTAGAACTGTATTGCTTGGGACCCTTGTCTACCA C?BC%DDDDDHHHHHHHHH
HHHGHHHHEHHHHHGHHHHHHHFHHHHHHHHFG?GEHHFHFFHFDHFHFBFHHHFFHHHHHHHHHHHHEHHEH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4C87
HWI-ST740_0001:1:1101:1099:2182#0 147 2 38975118 60 88M = 38974888 -318 TGTCCTTAAGACACTCTACTGATAAGATGTGAACAATCCAAACACAAGTAAGGAAAAAAAGTGTTACATACTGGAAATACCTCGATCC HHHHHFHHGHEHCHGHHHH
HHHHHHHHEHHHHHHHHHHFHHHHFHHHHHHHHHHHFHHHHFHFIGFGFFFHHHHHHHHDHHHHHHHHH XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1067:2205#0 83 8 96090111 60 12S80M = 96089991 -200 ATGAGCAAAAGGCAAGCCAGTCTAGGTGCATGGCCAGCCCCCCGAGATGGAGCTCATGGTGAGGGACCAGCCAAGTCAATCACATCTNCCTT %%%%%%%%%%%%%@;7@C<
BBCDCFEECDC5CCFCC4HHHHHDFDG?FHCFEEEEBFDCDDBGFF@FFHHHFHHHHHHHHHFDCDCD%AAAB XC:i:80 XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:75G4
HWI-ST740_0001:1:1101:1067:2205#0 163 8 96089991 60 88M = 96090111 200 TTGTAAAGGTCATGAGAAGTGCCTGTCCCTCCAAGGGTGCAAGGGTGACCAGAAGCAAGCTCTTAGGCATGGGTGGGCTTGCTGTGGA HHHHHHHHHHHHHHHHHEH
FHHHHHFHHHHHHHHHFHDHHFEHHHBFEFFGGGIGHHHHHHGHHHHEHHHHHHDHDGGEEHHBHCGFF XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1092:2208#0 99 16 23963265 60 92M = 23963410 233 GGTGNTGACCTGTTTGTCTCCCTGGCTGTCAGACTGTGAGAAACTTGAGGGCAGGGGCTGTACTTTATTCTTCTCTGTCTCTCTAGGGACTA >86;%8>===FHFHHHECH
FFEE?FFBFEEFHFEFEEHHH?DCD+FACBDF<EFECFE9C9=C?CD5C<0C<CC:6@0><DDDE<FCBDFCB XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4G87
HWI-ST740_0001:1:1101:1092:2208#0 147 16 23963410 60 88M = 23963265 -233 ACGTGGTATAAAACAGGTCTTGTGACTGAATGAGGGAATGAATGAAAAAGCCCTGTCCTGCCCTCCCTGCAGAGATGGGGTCTGCTGC @EAD>C?E<?DAADC==:H
EDDFDGFEFDCC9D@;@B75BDFBC@DFD?B?FFBFFFFDDDDD9D@FBHHBHEFGACGC@BDEFFDFG XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
HWI-ST740_0001:1:1101:1177:2226#0 99 1 182615131 60 92M = 182615381 338 TTTGCAAGCTGTATCTTTCTTAATGGCAGTTCCACTTCAGAAGTCATGAAGAACATCACCCAAGACTCTTTCTGGAAATGTAAGGTTAGGGT HHHHHHHHHHHHHHHHHHH
HHHGHHHHHG9DADADCFDBFEFE?FHHFBHFCHCHHEHFCD<DFDCAFEEGEBF>CBGEGDDFFE@E7?E@3 XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:92
HWI-ST740_0001:1:1101:1177:2226#0 147 1 182615381 60 88M = 182615131 -338 TCTCTCCTAAGCTGTGAGATCCCAGTGAGCAGAGCTGGCCACTACAAATCACAGAGTTGAGCCTAAGTCTTTCAGCTATTCCTCCCAG <=7D@D?DE:6EBG<BDF@
<DD69EEEE<CEEDBAIFGGGCGBEGFGFEGEGFHHHHFHHHHHGGGGBGHHFHHFHHHHEGHHHHHHH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:63C24
HWI-ST740_0001:1:1101:1066:2233#0 99 11 122934086 60 92M = 122934250 252 ACGANAGACCATACCGACGCTTTGAAAACGTGACTGAGCTGGTGCACAAAACAATGGTGCCTAGAATTTTGAATTGTGCAATGTTGTGCATG BABA%DDDDDGHHHHHHHH
HHHHHHHFHHHHHHHHHHHHHHHEHHCHHFHEHHHHHHEHFCEEGDFFFFHHFHHHHHHHHHHHEHHFHHFHH XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:4C87
HWI-ST740_0001:1:1101:1066:2233#0 147 11 122934250 60 88M = 122934086 -252 AAGCAGGCGAGGTAGCTGTTATTCCTATTTAGTAGATAAATAGGCACCGATGGGGGAAAAGATTTTTTAAGGCTACACCAAAAGAACT HHHHHHHGDHHHHHHHGGH
FHHHGHHHHDBHHHHHHHHHH@HHHHFHHHHHHHFHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHH XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:88
2012/8/17 Sigrid Rouam <sigrid...@gmail.com>
Dongjun Chung
Aug 18, 2012, 6:14:57 PM8/18/12
to mosaics_u...@googlegroups.com
Hi Sigrid,
Thanks for providing the example lines. Your sam file looks nice and it should work well with my perl script to process PET data. I attached the perl script to process PET data here.
Usage:
> perl process_readfiles_PET.pl [infile] [outdir] [format] [binsize] N N NULL
[infile]: name of aligned read file
[outdir]: directory that the bin-level file is exported to
[format]: format of aligned read file; either 'eland_result' or 'sam'
[binsize]: bin size
For example,
> perl process_readfiles_PET.pl example.sam . sam 150 N N NULL
Then, using the bin-level file obtained from this perl script, you can analyze your data using the following command lines:
> bin <- readBins( type = c("chip","input"), fileName=c("chip.txt_bin150.txt","input.txt_bin150.txt") )
> fit <- mosaicsFit( bin )
> peak <- mosaicsPeak( fit )
> export( peak, type="bed", filename="peak.bed" )
Please just let me know if you have any questions.
Thanks,
Dongjun
Thanks for providing the example lines. Your sam file looks nice and it should work well with my perl script to process PET data. I attached the perl script to process PET data here.
Usage:
> perl process_readfiles_PET.pl [infile] [outdir] [format] [binsize] N N NULL
[infile]: name of aligned read file
[outdir]: directory that the bin-level file is exported to
[format]: format of aligned read file; either 'eland_result' or 'sam'
[binsize]: bin size
For example,
> perl process_readfiles_PET.pl example.sam . sam 150 N N NULL
Then, using the bin-level file obtained from this perl script, you can analyze your data using the following command lines:
> bin <- readBins( type = c("chip","input"), fileName=c("chip.txt_bin150.txt","input.txt_bin150.txt") )
> fit <- mosaicsFit( bin )
> peak <- mosaicsPeak( fit )
> export( peak, type="bed", filename="peak.bed" )
Please just let me know if you have any questions.
Thanks,
Dongjun
Sigrid Rouam
Aug 19, 2012, 1:42:39 AM8/19/12
to mosaics_u...@googlegroups.com
Hi Dongjun,
--
Thank you very much. I will try.
Regards,
Sigrid
--
Sigrid Rouam
Aug 20, 2012, 9:13:29 PM8/20/12
to mosaics_u...@googlegroups.com
Hi Dongjun,
I would like to try your perl script, but I could not find it in attachments. Could you send it again?
I have another question regarding the preprocessing of the mappability and GC content files into bin level files. What parameters should I use for the PET data?
Thank you!
Sigrid
I would like to try your perl script, but I could not find it in attachments. Could you send it again?
I have another question regarding the preprocessing of the mappability and GC content files into bin level files. What parameters should I use for the PET data?
Thank you!
Sigrid
2012/8/19 Dongjun Chung <dongju...@gmail.com>
Dongjun Chung
Aug 21, 2012, 7:57:58 PM8/21/12
to mosaics_u...@googlegroups.com
Hi Sigrid,
I put the perl script to process PET ChIP-seq data, "process_readfiles_PET_v2.pl", here:
https://www.dropbox.com/sh/rt2s3bv3b9mfto0/wfjRUaXQrl
Regarding the second question, at this point, we did not develop a script to process mappability and GC content scores for PET data yet. Although it is not perfect, you can use mappability and GC content scores for SET data as an approximation. You can also try two-sample analysis without using mappability and GC content if you have matched control sample. I will let you know if we have any updates regarding this issue.
Thanks,
Dongjun
I put the perl script to process PET ChIP-seq data, "process_readfiles_PET_v2.pl", here:
https://www.dropbox.com/sh/rt2s3bv3b9mfto0/wfjRUaXQrl
Regarding the second question, at this point, we did not develop a script to process mappability and GC content scores for PET data yet. Although it is not perfect, you can use mappability and GC content scores for SET data as an approximation. You can also try two-sample analysis without using mappability and GC content if you have matched control sample. I will let you know if we have any updates regarding this issue.
Thanks,
Dongjun
Sigrid Rouam
Sep 5, 2012, 2:15:25 AM9/5/12
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