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翁靖傑
,
Hunter Richards
2
8/10/15
pure Biochemistry lab want to do ATAC-seq?
There is nothing special about ATAC-seq that would require a different analytical pipeline that is
unread,
pure Biochemistry lab want to do ATAC-seq?
There is nothing special about ATAC-seq that would require a different analytical pipeline that is
8/10/15
helpneeded
8/10/15
genome table for arabidopsis
Hello, I am very new to chip-seq data. I have run bowite with my illumine reads on remote server. Now
unread,
genome table for arabidopsis
Hello, I am very new to chip-seq data. I have run bowite with my illumine reads on remote server. Now
8/10/15
nultontj
, …
Federico Gaiti
16
7/1/15
0 peaks found using QuEST
Hi all, I've been trying to run QuEST. I am working on a sponge species I have thousands of
unread,
0 peaks found using QuEST
Hi all, I've been trying to run QuEST. I am working on a sponge species I have thousands of
7/1/15
Yi Li
, …
Federico Gaiti
4
7/1/15
QuEST found 0 peaks in output
Hi all, I've been trying to run QuEST. I am working on a sponge species I have thousands of
unread,
QuEST found 0 peaks in output
Hi all, I've been trying to run QuEST. I am working on a sponge species I have thousands of
7/1/15
Anton
,
Liang
5
6/9/15
How to use QuEST for ATAC-Seq data
Hi Liang, when you see the peaks, is it by uploading wig files from QuEST? Try repeating analysis
unread,
How to use QuEST for ATAC-Seq data
Hi Liang, when you see the peaks, is it by uploading wig files from QuEST? Try repeating analysis
6/9/15
Liang
,
Anton
2
6/3/15
QuEST Parameters for ATAC-Seq
I posted the answer to a different thread. You can post there if you have more questions. Thanks,
unread,
QuEST Parameters for ATAC-Seq
I posted the answer to a different thread. You can post there if you have more questions. Thanks,
6/3/15
Ping Wu
, …
Hunter Richards
11
5/28/15
question from Ping Wu
Hi Anton, When I rebuilt the genome table by replacing the \t with a space, it works now. Thanks,
unread,
question from Ping Wu
Hi Anton, When I rebuilt the genome table by replacing the \t with a space, it works now. Thanks,
5/28/15
Shan Jiang
9/12/14
problem with wig file
Hello QuEST Group, I uploaded ChIP_normalized_wig file into UCSC genome browser to show peaks.
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problem with wig file
Hello QuEST Group, I uploaded ChIP_normalized_wig file into UCSC genome browser to show peaks.
9/12/14
赵信
,
Anton
2
7/29/14
Error running QuEST 2.4
Hi Xin, I've seen this error before, but I didn't have enough info from the user to tell what
unread,
Error running QuEST 2.4
Hi Xin, I've seen this error before, but I didn't have enough info from the user to tell what
7/29/14
rli...@ucr.edu
,
Anton
2
6/3/14
how to generate genome table
Hi Ruidong, you can provide a path to a directory containing individual fasta files with chromosomes
unread,
how to generate genome table
Hi Ruidong, you can provide a path to a directory containing individual fasta files with chromosomes
6/3/14
Theodore Georgomanolis
,
Anton
9
4/17/14
error running ./generate_QuEST_parameters.pl
Hi Theodore, thank you for your patience. It seems I found a small bug in genome table generation,
unread,
error running ./generate_QuEST_parameters.pl
Hi Theodore, thank you for your patience. It seems I found a small bug in genome table generation,
4/17/14
Antonio Gomes
,
Anton
5
4/14/14
Is GABP GABPa or GABPb?
Hi Anton, Thank you very much for the reply. This is all I need. Best, Antonio On Apr 14, 2014 2:10
unread,
Is GABP GABPa or GABPb?
Hi Anton, Thank you very much for the reply. This is all I need. Best, Antonio On Apr 14, 2014 2:10
4/14/14
Theodore Georgomanolis
,
Anton
4
4/14/14
error while running QuEST_2.4
See my response to another thread. On Friday, April 11, 2014 8:16:57 AM UTC-7, Theodore Georgomanolis
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error while running QuEST_2.4
See my response to another thread. On Friday, April 11, 2014 8:16:57 AM UTC-7, Theodore Georgomanolis
4/14/14
timdeme...@gmail.com
,
Anton
2
3/28/14
Paired end data: amount of identified peaks depends on peak shift estimate
Hi Tim, the number of peaks does not strongly depend on the peak shift for small values of peak shift
unread,
Paired end data: amount of identified peaks depends on peak shift estimate
Hi Tim, the number of peaks does not strongly depend on the peak shift for small values of peak shift
3/28/14
harukao
, …
Anton
15
11/2/13
Error with generate_QuEST_parameters.pl
Are you using the latest QuEST version 2.4? You can grab it here: http://www-hsc.usc.edu/~valouev/
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Error with generate_QuEST_parameters.pl
Are you using the latest QuEST version 2.4? You can grab it here: http://www-hsc.usc.edu/~valouev/
11/2/13
Archibald Perkins
, …
Anton
5
10/29/13
BED files for GREAT program
To see the first 10 lines try this: head -10 yourfile.bed To count the number of lines wc -l yourfile
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BED files for GREAT program
To see the first 10 lines try this: head -10 yourfile.bed To count the number of lines wc -l yourfile
10/29/13
yif...@gmail.com
, …
Anton Valouev
4
10/9/13
script: output_genomic_regions_from_calls.pl
There is a bed file for the peak positions and another bed file for the region positions. See the
unread,
script: output_genomic_regions_from_calls.pl
There is a bed file for the peak positions and another bed file for the region positions. See the
10/9/13
jlmlj
, …
Hunter Richards
17
10/8/13
visualization of output of QuEST
$ sed 's/chr=1/chr=chr1/g' file-in > file-out "s" means substitute The string in
unread,
visualization of output of QuEST
$ sed 's/chr=1/chr=chr1/g' file-in > file-out "s" means substitute The string in
10/8/13
Hunter Richards
,
Anton
3
9/11/13
very large datasets
Yeah, the 30GB swap I would up using was enough, but it was slow; it took about 30 minutes just to
unread,
very large datasets
Yeah, the 30GB swap I would up using was enough, but it was slow; it took about 30 minutes just to
9/11/13
Matthew McCormack
, …
Anton
14
8/26/13
format for input data to QuEST
Does it accept your files though? QuEST prints the progress while parsing your input files and you
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format for input data to QuEST
Does it accept your files though? QuEST prints the progress while parsing your input files and you
8/26/13
swa...@gmail.com
,
Anton
2
8/20/13
convert bed to wig file
Hi Emma, yes, it is possible. Check out the QuEST tutorial. QuEST provides normalized wig score files
unread,
convert bed to wig file
Hi Emma, yes, it is possible. Check out the QuEST tutorial. QuEST provides normalized wig score files
8/20/13
KL
,
Anton
4
8/16/13
Negative peak shift in positive control region
KL, this may indeed be a bug of some sort. Can you share with me (in an email) a QuEST file with
unread,
Negative peak shift in positive control region
KL, this may indeed be a bug of some sort. Can you share with me (in an email) a QuEST file with
8/16/13
anu
,
Anton
2
8/14/13
QuEST tutorial unavailable
http://www-hsc.usc.edu/~valouev/QuEST/QuEST.html On Wednesday, August 29, 2012 12:18:45 AM UTC-7, anu
unread,
QuEST tutorial unavailable
http://www-hsc.usc.edu/~valouev/QuEST/QuEST.html On Wednesday, August 29, 2012 12:18:45 AM UTC-7, anu
8/14/13
ankit arora
,
Anton
2
8/14/13
Error while rexecuting QuEST.
Bowtie format is no longer supported. It might have changed since last time I looked at it. The best
unread,
Error while rexecuting QuEST.
Bowtie format is no longer supported. It might have changed since last time I looked at it. The best
8/14/13
nultontj
7/29/13
no peaks found by using QuEST
I'm using QuEST to analyze our lab's chIP-seq data and comparing it with the analysis done by
unread,
no peaks found by using QuEST
I'm using QuEST to analyze our lab's chIP-seq data and comparing it with the analysis done by
7/29/13
Mingyang Cai
, …
Anton
4
7/16/13
abnormal normalized & unnormalized wig files
Yes, you can exit after configuration script and edit those files. Then run run_QuEST_with_param_file
unread,
abnormal normalized & unnormalized wig files
Yes, you can exit after configuration script and edit those files. Then run run_QuEST_with_param_file
7/16/13
dinodi...@gmail.com
,
Anton
2
7/16/13
Calling peaks in repeats region ChIP-Seq
Hi Kushal, not an expert on Bowtie unfortunately. Perhaps refer to their manual to determine how to
unread,
Calling peaks in repeats region ChIP-Seq
Hi Kushal, not an expert on Bowtie unfortunately. Perhaps refer to their manual to determine how to
7/16/13
Hunter Richards
,
Anton Valouev
3
7/8/13
error code 9
Hi Anton, It was a disk-space issue. I only had a few hundred GBs left on the disk. I added another
unread,
error code 9
Hi Anton, It was a disk-space issue. I only had a few hundred GBs left on the disk. I added another
7/8/13
pfa...@gmail.com
,
Anton
3
3/21/13
reading of eland result files in quest
thanks for the reply i will waste no more time. earlier i used samtools-0.1.7a/misc/export2sam.pl to
unread,
reading of eland result files in quest
thanks for the reply i will waste no more time. earlier i used samtools-0.1.7a/misc/export2sam.pl to
3/21/13
pfa...@gmail.com
,
Anton
3
1/7/13
query regarding bedgraph output
Thanks, these are warnings, not a big deal. In regard to your earlier question - you do not need to
unread,
query regarding bedgraph output
Thanks, these are warnings, not a big deal. In regard to your earlier question - you do not need to
1/7/13