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12/28/18

Hi Tao, Does macs2 applicable to rampage data to call peaks? Is there any pro and con to apply it to

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Hi Tao, Does macs2 applicable to rampage data to call peaks? Is there any pro and con to apply it to

12/28/18

Mariam, … Moshe Olshansky9

10/2/18

Unusual negative likelihood ratios using bdgdiff

Hi Tao, Thank you. I am very busy till Wednesday the 10th but after this I will try what you said and

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Unusual negative likelihood ratios using bdgdiff

Hi Tao, Thank you. I am very busy till Wednesday the 10th but after this I will try what you said and

10/2/18

6/4/18

Question: less significant summits were called, but more significant ones were neglected (macs2 callpeak -t myfile.bed -f BED --nomodel extsize 10 -q 0.02 --call-summits)

Dear you who could help, I have a bed file in which all the reads are with fixed length of 10. To

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Question: less significant summits were called, but more significant ones were neglected (macs2 callpeak -t myfile.bed -f BED --nomodel extsize 10 -q 0.02 --call-summits)

Dear you who could help, I have a bed file in which all the reads are with fixed length of 10. To

6/4/18

Moshe Olshansky

4/18/18

Statistical model implementation in MACS

Hello Tao, Is there any possibility to get more detail about the actual implementation of the

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Statistical model implementation in MACS

Hello Tao, Is there any possibility to get more detail about the actual implementation of the

4/18/18

Abhishek Singh, John Urban5

2/15/18

with or without --nomodel

Yes, I agree that an overlap from another peak caller will be more helpful. On Thu, Feb 15, 2018 at 6

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with or without --nomodel

Yes, I agree that an overlap from another peak caller will be more helpful. On Thu, Feb 15, 2018 at 6

2/15/18

Abhishek Singh, … Moshe Olshansky5

2/9/18

Good number of reads but very few peaks

So how many peaks did you get? We also have an old P300 ChIP-Seq (mouse) for which we could not do

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Good number of reads but very few peaks

So how many peaks did you get? We also have an old P300 ChIP-Seq (mouse) for which we could not do

2/9/18

Anupriya Verma, Moshe Olshansky2

9/28/17

Narrow & Broad peaks from 'macs2 bdgdiff'

Hi Anupriya, I think that the only parameter which is relevant in bdgdiff is -g which says how far

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Narrow & Broad peaks from 'macs2 bdgdiff'

Hi Anupriya, I think that the only parameter which is relevant in bdgdiff is -g which says how far

9/28/17

julie dubois, Moshe Olshansky7

9/19/17

Macs2 callpeak ValueError: max() arg is an empty sequence

Dear Moshe, Thanks a lot for the time you took for this issue. I hope Tao can explain this bug too.

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Macs2 callpeak ValueError: max() arg is an empty sequence

Dear Moshe, Thanks a lot for the time you took for this issue. I hope Tao can explain this bug too.

9/19/17

Anupriya Verma, … Ian Donaldson3

9/18/17

Extension size problem.

Just to check - is d = 292 or 213? Julie is right, i think, but I am wondering if you set extsize

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Extension size problem.

Just to check - is d = 292 or 213? Julie is right, i think, but I am wondering if you set extsize

9/18/17

5/6/17

macs2 refinepeak Output File

Hi, I'm running a "macs2.real refinepeak" command to define summit positions for a BED

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macs2 refinepeak Output File

Hi, I'm running a "macs2.real refinepeak" command to define summit positions for a BED

5/6/17

laurenz...@hotmail.com

2/28/17

MACS2: summit calculations

Dear T. Liu and colleagues, I had a question regarding the summit calculation in MACS2. I've

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MACS2: summit calculations

Dear T. Liu and colleagues, I had a question regarding the summit calculation in MACS2. I've

2/28/17

11/29/16

The scores of 5th column (integer score for display) in macs2 NAME_peaks.narrowPeak file are larger than 1000

Hi, I have asked this question on Biostars, but nobody answered me. I use macs2 for peak calling, and

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The scores of 5th column (integer score for display) in macs2 NAME_peaks.narrowPeak file are larger than 1000

Hi, I have asked this question on Biostars, but nobody answered me. I use macs2 for peak calling, and

11/29/16

Xi Chen, Ian Donaldson3

11/9/16

possible --call-troughs functionality

Thanks, Ian. HOMER's findPeak also has this function (-nfr flag), but I have not personally tried

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possible --call-troughs functionality

Thanks, Ian. HOMER's findPeak also has this function (-nfr flag), but I have not personally tried

11/9/16

wendy, Ian Donaldson2

11/3/16

Help!!!! masc2, paired-end(BAMPE)

Apologies for not answering your questions directly, I do not know about the effect of --nolambda.

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Help!!!! masc2, paired-end(BAMPE)

Apologies for not answering your questions directly, I do not know about the effect of --nolambda.

11/3/16

Max Qian, Timothy Parnell3

10/13/16

macs2 pileup and callpeak

Hi Tim, Yes, you are absolutely right. That's definite a solution. But, I have to go back and

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macs2 pileup and callpeak

Hi Tim, Yes, you are absolutely right. That's definite a solution. But, I have to go back and

10/13/16

rpsilos, Anna Battenhouse2

9/19/16

P value cutoff for output file

So this comes back to what the effect of a less stringent P-value threshold is in MACS2. One might

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P value cutoff for output file

So this comes back to what the effect of a less stringent P-value threshold is in MACS2. One might

9/19/16

Stéphanie Rialle

9/19/16

the max duplicate tags is not used for control sample

Hi all, I am using MACS2 2.1.1.20160309 and I have a problem regarding the filtering of duplicate

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the max duplicate tags is not used for control sample

Hi all, I am using MACS2 2.1.1.20160309 and I have a problem regarding the filtering of duplicate

9/19/16

cnov...@gmail.com

9/19/16

Discrepancy in uniquely mapped reads between samtools and macs (1.4 or 2)

Hi Tao, I have noticed a discrepancy in the uniquely mapped reads identified by samtools or either

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Discrepancy in uniquely mapped reads between samtools and macs (1.4 or 2)

Hi Tao, I have noticed a discrepancy in the uniquely mapped reads identified by samtools or either

9/19/16

Aarthi Mohan, … Ian Donaldson5

9/6/16

Procedure to generate control pileup for Paired-end data

Hi Ian and Moshe, Thanks for your responses. I have followed the same Biostar post to generate the

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Procedure to generate control pileup for Paired-end data

Hi Ian and Moshe, Thanks for your responses. I have followed the same Biostar post to generate the

9/6/16

Moshe Olshansky

8/26/16

how does bdgcmp work?

Dear Tao, Thank you very much for posting "Advanced: Call peaks using MACS2 subcommands". I

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how does bdgcmp work?

Dear Tao, Thank you very much for posting "Advanced: Call peaks using MACS2 subcommands". I

8/26/16

Moshe Olshansky, Timothy Parnell4

8/25/16

interpretation of bdgdiff results

Hi Tim, Thank you for your note. I understand that the pileup files are scaled. But what happens then

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interpretation of bdgdiff results

Hi Tim, Thank you for your note. I understand that the pileup files are scaled. But what happens then

8/25/16

Abhishek Singh, … John Urban3

8/17/16

Effective genome size for rat and pig

To add to that -- you can probably use the sum of the sequence lengths or 0.8*sum_lengths (for

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Effective genome size for rat and pig

To add to that -- you can probably use the sum of the sequence lengths or 0.8*sum_lengths (for

8/17/16

8/9/16

MACS2.1.1 apparently breaks with large numbers of reads: [ValueError: cannot resize this array: it does not own its data]

Version 2.1.0.20140616 was able to run with the full dataset using --broad.

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MACS2.1.1 apparently breaks with large numbers of reads: [ValueError: cannot resize this array: it does not own its data]

Version 2.1.0.20140616 was able to run with the full dataset using --broad.

8/9/16

Aarthi Mohan, Timothy Parnell3

7/28/16

bdgpeakcall vs callpeak

Hi Timothy, Thanks for the reply. The default behaviour of callpeak is to use the maximum value from

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bdgpeakcall vs callpeak

Hi Timothy, Thanks for the reply. The default behaviour of callpeak is to use the maximum value from

7/28/16

7/27/16

macs2 pileup command gives different values for BAM vs BED

Ok, I figured it out. macs2 pileup will only choose the first mate for extension, when a BAM file is

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macs2 pileup command gives different values for BAM vs BED

Ok, I figured it out. macs2 pileup will only choose the first mate for extension, when a BAM file is

7/27/16

Aarthi Mohan, Moshe Olshansky3

6/18/16

Difference b/w version 2.1.0.20150731 and version 2.1.1.20160309

Hi Moshe, I am using BAMPE, and still see a huge difference in broad peak call numbers between the

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Difference b/w version 2.1.0.20150731 and version 2.1.1.20160309

Hi Moshe, I am using BAMPE, and still see a huge difference in broad peak call numbers between the

6/18/16

Moshe Olshansky, Tao Liu3

4/11/16

Thank you, it works!!! On Monday, April 11, 2016 at 1:34:36 PM UTC+10, Moshe Olshansky wrote: Hello,

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Thank you, it works!!! On Monday, April 11, 2016 at 1:34:36 PM UTC+10, Moshe Olshansky wrote: Hello,

4/11/16

Anupriya Verma, Tao Liu2

3/9/16

Error with bdg2bw.

Hi Anupriya, My guess is that the chromosome names in bdg file are like '1, 2, 3…' but the

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Error with bdg2bw.

Hi Anupriya, My guess is that the chromosome names in bdg file are like '1, 2, 3…' but the

3/9/16

3/9/16

Questions about the published paper

Hi Tao, In your paper 'Model-based Analysis of ChIP-Seq', the FDR, motif occurrence and

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Questions about the published paper

Hi Tao, In your paper 'Model-based Analysis of ChIP-Seq', the FDR, motif occurrence and

3/9/16

2/18/16

Re: [macs-announscement] ValueError: cannot resize this array: it does not own its data

Hi Alex, I have never seen such error before. Sometimes, if the upgrades of the same software on the

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Re: [macs-announscement] ValueError: cannot resize this array: it does not own its data

Hi Alex, I have never seen such error before. Sometimes, if the upgrades of the same software on the

2/18/16

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