User: gewa

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gewa0
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Posts by gewa

<prev • 7 results • page 1 of 1 • next >
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Comment: C: deeptools bamcompare/bamcoverage merging bins?
... I will try this and update with results, thanks! Also, is there any way you could please explain the calculation for the scale factor? I'm having trouble understanding where the 8 comes from, and why to use IDXstats. Thanks so much again! ...
written 1 day ago by gewa0
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deeptools bamcompare/bamcoverage merging bins?
... Hi all, I am currently using deepTools to process some chip-seq data and need a sanity check as to how to interpret/deal with the output, as I am not sure after reading the docs. I have some alignment files from multiple replicates of a ChIP-seq experiment targeting a histone mark. What I need to do ...
deeptools chip-seq written 1 day ago by gewa0 • updated 1 day ago by ATpoint5.5k
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ChIP-seq normalization for input with RPKM
... Hi all, I'm currently trying to work off part of a paper (found [here][1]) involving processing some ChIP-seq data for histone modifications (ie H3K4me1). At one point (under "Histone Modication Inputs, Normalization, Preprocessing") the authors say: > The ChIP-seq reads of these histone mod ...
chip-seq written 6 days ago by gewa0 • updated 5 days ago by ATpoint5.5k
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Comment: C: Persistent parse and truncation errors sorting BAM files with samtools
... I have the same md5sum for my file -- I am assuming then that this issue is with my samtools version and will try 1.5. Thanks so much for the help! ...
written 13 days ago by gewa0
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Comment: C: Persistent parse and truncation errors sorting BAM files with samtools
... Hi, Yes, it is already coordinate sorted but I am unsure about all of the reference sequences used and wanted to ensure I could re-sort it if necessary. The file I am using specifically is: https://www.encodeproject.org/files/ENCFF592KJQ/@@download/ENCFF592KJQ.bam The experiment where the file is c ...
written 14 days ago by gewa0
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Comment: C: Persistent parse and truncation errors sorting BAM files with samtools
... Hey, I updated the original post with this information + the (improved) results of more troubleshooting (which was really just using the most recent version of samtools, 1.7, available). Let me know if I can add anything else that would be helpful ...
written 15 days ago by gewa0
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Persistent parse and truncation errors sorting BAM files with samtools
... Hi, I am using samtools version 1.7 to try and sort a BAM file but am running into a persistent error I can't understand/resolve with Google. The job completes, with the exception that the output (sorted) BAM file's header begins with the warning that: `[W::bam_hdr_read] EOF marker is absent. The ...
software error alignment written 16 days ago by gewa0 • updated 15 days ago by finswimmer3.6k

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