User: aebmad

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aebmad30
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Posts by aebmad

<prev • 8 results • page 1 of 1 • next >
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Comment: C: filter reads in BAM having a tag
... Thanks for mentioning sambamba and samsift, I will take a look. ...
written 8 weeks ago by aebmad30
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Answer: A: filter reads in BAM having a tag
... It turns out the samtools dev team was [already working][1] on this feature, which will be available in the next release (in the meantime it can be used pulling the develop branch). `samtools view -d TAG` does the trick. [1]: https://github.com/samtools/samtools/pull/1339 ...
written 8 weeks ago by aebmad30
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filter reads in BAM having a tag
... Anyone has a simple solution for filtering reads in a BAM/SAM file having a certain TAG? This came up trying to filter out reads from 10x without a proper CB tag defined (which is causing troubles in downstream analysis tools). I'm surprised there is no built-in command in `samtools` for doing this ...
alignment samtools written 8 weeks ago by aebmad30 • updated 8 weeks ago by jkbonfield470
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Answer: A: Deeptools: computeMatrix - Traceback
... A **temporary solution** is to **downgrade deeptools** to version 2.1.0 (I have not tried all the releases, just so happens that I was using this before I recently had to reinstall conda and all the packages). Hopefully this also gives some hints to the dev team (thanks for this great toolkit by the ...
written 4.2 years ago by aebmad30
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Comment: C: Deeptools: computeMatrix - Traceback
... I'm having the exact same issue using the latest deeptools version from bioconda. Before trying the very latest development version of deeptools, did you find already a solution for this? Thanks! ...
written 4.2 years ago by aebmad30
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Comment: C: Example cwl workflow (for v1.0)?
... Hi Michael, I'm looking into upgrading the workflows that we have at Duke-GCB from version draft3 to 1.0. Is there any document that specifies the differences introduced by v1.0? I can't find it. Thanks! ...
written 4.5 years ago by aebmad30
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Comment: C: Parse Fastq File - Pad Reads With N'S
... This is an old thread but still.. any reason why you pad the quality line with "2"s? Wouldn't the lowest quality score "!" make more sense here? ...
written 5.4 years ago by aebmad30
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Answer: A: Where To Download Hg19 Gene Annotation, Transcript Annotation And Cdna Fasta Fil
... For the transcript annotation file, I use the genePredToGtf script from UCSC which allows you to create a GTF annotation file. You can find a detailed explanation of how to download and use the script here: http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format Alex ...
written 5.7 years ago by aebmad30

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