deepTools

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This is the mailing list for bug reports and comments on the deepTools package.

Feel free to respond to questions by other users if you've dealt with similar issues!

Please check our package documentation here that includes several FAQs on Galaxy-related as well as typical command-line issues.

If you have a github account, you can also directly report issues at deepTools' github page.

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1/23/20

New version (3.3.2), new support venue, and other updates

Hi everyone, I'm happy to announce version 3.3.2 of deepTools, which is already available on PyPI

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New version (3.3.2), new support venue, and other updates

Hi everyone, I'm happy to announce version 3.3.2 of deepTools, which is already available on PyPI

1/23/20

christianma...@u.northwestern.edu, Devon Ryan2

1/22/20

plotprofile multiple replicates from two groups on a single plot

Hi Christian, You can use plotProfile or plotHeatmap as normal and use the `--perGroup` option to get

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plotprofile multiple replicates from two groups on a single plot

Hi Christian, You can use plotProfile or plotHeatmap as normal and use the `--perGroup` option to get

1/22/20

Press Report Study

1/15/20

Press Report Study

Dear Colleagues, We kindly invite you to participate in our short study regarding research press

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Press Report Study

Dear Colleagues, We kindly invite you to participate in our short study regarding research press

1/15/20

Aditi Singh, … adit...@gmail.com3

1/15/20

ComputeMatrix is not complete even in 3 days of running

Thanks Devon, I am using 20gb memory and 8 cores. Will increase as suggested. Thanks for the response

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ComputeMatrix is not complete even in 3 days of running

Thanks Devon, I am using 20gb memory and 8 cores. Will increase as suggested. Thanks for the response

1/15/20

Rebekah Rashford, Devon Ryan11

1/8/20

plotProfile not plotting single image from multiple inputs

Awesome--thank you so much for all of your help! ------------------------------------------------

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plotProfile not plotting single image from multiple inputs

Awesome--thank you so much for all of your help! ------------------------------------------------

1/8/20

Mehrnush Forutan, Devon Ryan2

1/7/20

deeptools/3.3.1

DeepTools merges bases that have the same coverage since the output is then smaller but otherwise

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deeptools/3.3.1

DeepTools merges bases that have the same coverage since the output is then smaller but otherwise

1/7/20

Ashley Conard, … Devon Ryan9

1/7/20

Huge confusion, please advise

If you want a log2 change then you can use bigwigCompare, but then you'll need something for the

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Huge confusion, please advise

If you want a log2 change then you can use bigwigCompare, but then you'll need something for the

1/7/20

BADGERJL, Devon Ryan3

12/31/19

Thanks for the expert input! I was thinking something similar, so glad to know I'm on the right

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Thanks for the expert input! I was thinking something similar, so glad to know I'm on the right

12/31/19

Ashley S Doane, Vivek Bhardwaj5

12/17/19

bed12 for pygenomeTracks to show gene name

Hi again, So this worked and generated a plot with genes that have intron/exon information and named

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bed12 for pygenomeTracks to show gene name

Hi again, So this worked and generated a plot with genes that have intron/exon information and named

12/17/19

Iddir Yasmine, Devon Ryan2

12/10/19

Deeptools questions

Hi Yasmine, bamCoverage has a few options for normalization, of which usually RPKM or RPGC (aka 1x

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Deeptools questions

Hi Yasmine, bamCoverage has a few options for normalization, of which usually RPKM or RPGC (aka 1x

12/10/19

Daniel Bsteh, Devon Ryan3

12/10/19

Bamcoverage tool normalizing for sequencing depth and internal spike-in scaling factor at the same time

Okay thanks for your help! On 12/9/19, 11:08 PM, "Devon Ryan" <dpr...@dpryan.com>

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Bamcoverage tool normalizing for sequencing depth and internal spike-in scaling factor at the same time

Okay thanks for your help! On 12/9/19, 11:08 PM, "Devon Ryan" <dpr...@dpryan.com>

12/10/19

Marina Veil, … Hunter Richards3

12/6/19

plotprofile adjustments

Apologies if this is too obvious but since there likely isn't a way for any program to really

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plotprofile adjustments

Apologies if this is too obvious but since there likely isn't a way for any program to really

12/6/19

11/28/19

All published papers in worldwide indexing

International Refereed Journal of Engineering and Science (IRJES) Call for paper: November 2019 Issue

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All published papers in worldwide indexing

International Refereed Journal of Engineering and Science (IRJES) Call for paper: November 2019 Issue

11/28/19

Dr A. Ismail, Devon Ryan2

11/14/19

looking for support

The tagAlign format hasn't been used in many years, I suggest you use a more modern peak caller

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looking for support

The tagAlign format hasn't been used in many years, I suggest you use a more modern peak caller

11/14/19

António Miguel de Jesus Domingues, Devon Ryan3

11/11/19

multiBigwigSummary with outRawCounts - output all fields from input bed

Hi Devon, thank you for point me in the direction of the solution. In the meantime I thought of a

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multiBigwigSummary with outRawCounts - output all fields from input bed

Hi Devon, thank you for point me in the direction of the solution. In the meantime I thought of a

11/11/19

Siyao Gu, Devon Ryan4

11/4/19

Trouble with Installation

It sounds like you're using python2, which has reached its end of life and is no longer supported

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Trouble with Installation

It sounds like you're using python2, which has reached its end of life and is no longer supported

11/4/19

Beatriz Cardoso de Toledo, Devon Ryan3

11/4/19

Bigwig generation, Normalization by input leads to strange result

Good evening, I generated new images of other regions. One thing I noticed was that the files were

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Bigwig generation, Normalization by input leads to strange result

Good evening, I generated new images of other regions. One thing I noticed was that the files were

11/4/19

11/4/19

error message :E::hts_hopen

Hi, I am trying to run deeptools with Sorted bam files converted to Bam.bai files (using samtools )

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error message :E::hts_hopen

Hi, I am trying to run deeptools with Sorted bam files converted to Bam.bai files (using samtools )

11/4/19

Jiang Xu, Vivek Bhardwaj3

10/28/19

about the same_fragment filter in hicBuildMatrix

Hi Vivek, Thank you for your explanation. If I didn't set the RE option? What restriction site

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about the same_fragment filter in hicBuildMatrix

Hi Vivek, Thank you for your explanation. If I didn't set the RE option? What restriction site

10/28/19

Jiang Xu, Vivek Bhardwaj5

10/24/19

about HiC data without restriction cutting and abnormally high outward pairs

Hi Vivek, 1. Do you have a systematic principle on what pairs will be discarded, in addtion to like

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about HiC data without restriction cutting and abnormally high outward pairs

Hi Vivek, 1. Do you have a systematic principle on what pairs will be discarded, in addtion to like

10/24/19

10/23/19

what is the correct parameter for --doTestRun in hicBuildMatrix

Also, if I do not include '--doTestRun option', can I still use '--doTestRunlines option

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what is the correct parameter for --doTestRun in hicBuildMatrix

Also, if I do not include '--doTestRun option', can I still use '--doTestRunlines option

10/23/19

Jiang Xu, Devon Ryan3

10/23/19

about how to use bamCoverage

Thanks a lot! On Mon, Oct 21, 2019 at 2:10 PM Devon Ryan <dpr...@dpryan.com> wrote: Hi Jiang Xu

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about how to use bamCoverage

Thanks a lot! On Mon, Oct 21, 2019 at 2:10 PM Devon Ryan <dpr...@dpryan.com> wrote: Hi Jiang Xu

10/23/19

jingyu...@brown.edu, … Thomas Manke5

10/16/19

Heatmap for differential regions identified by DiffBind - Interpret

Hi, Thomas, Thank you very much for the suggestion! I will try K-clustering in deeptools! Do you

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Heatmap for differential regions identified by DiffBind - Interpret

Hi, Thomas, Thank you very much for the suggestion! I will try K-clustering in deeptools! Do you

10/16/19

Yung-Chih Lai, Devon Ryan8

10/11/19

Importing the multiarray numpy extension module failed

Dear Devon, The deepTools is a vital bioinformatics tool to analyze our RNAseq, ChIPseq, and ATACseq

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Importing the multiarray numpy extension module failed

Dear Devon, The deepTools is a vital bioinformatics tool to analyze our RNAseq, ChIPseq, and ATACseq

10/11/19

Ranjita Thapa, Devon Ryan2

10/10/19

peak calling from chip seq data

You can do this by creating a bigWig from the macs peaks (use 1 for regions where there's a peak

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peak calling from chip seq data

You can do this by creating a bigWig from the macs peaks (use 1 for regions where there's a peak

10/10/19

10/10/19

peak call coverage from chip seq data

Hi, I have a question on peak call using deeptools. I am doing peak call from chip seq data. I do

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peak call coverage from chip seq data

Hi, I have a question on peak call using deeptools. I am doing peak call from chip seq data. I do

10/10/19

10/7/19

棺至珊墓萃磕聆赠晤晋 bgbqi

runfei.liao He acted。 as he wrote！ like a brother。 13815310705zqk 赖帛榕 and asking permission

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棺至珊墓萃磕聆赠晤晋 bgbqi

runfei.liao He acted。 as he wrote！ like a brother。 13815310705zqk 赖帛榕 and asking permission

10/7/19

Saurabh Pradhan, Devon Ryan3

10/5/19

issue with heatmap plotting using kmeans

Great !! Thanks Devon, It worked well for me. I did not realise it. Thanking you with Best wishes

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issue with heatmap plotting using kmeans

Great !! Thanks Devon, It worked well for me. I did not realise it. Thanking you with Best wishes

10/5/19

9/30/19

Rank #1 in Google Search

Dear Business owner, I am in the business of helping people develop and Rank their websites.

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Rank #1 in Google Search

Dear Business owner, I am in the business of helping people develop and Rank their websites.

9/30/19

Jiang Xu, Vivek Bhardwaj6

9/30/19

About how to convert .h5 file to csv file

Hi Vivek, Thank you so much for you help! Best! Jiang On Sun, Sep 29, 2019 at 3:10 AM Vivek Bhardwaj

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About how to convert .h5 file to csv file

Hi Vivek, Thank you so much for you help! Best! Jiang On Sun, Sep 29, 2019 at 3:10 AM Vivek Bhardwaj

9/30/19

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