User: rbronste
rbronste • 200
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Posts by rbronste
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... After merging 6 bam files (samtools merge) I attempted to look at the read depth within a specific set of intervals and got the following error, not sure exactly why expect maybe the merge tool takes a sam and not a bam file?
samtools depth -b --bed /sonas-hs/tollkuhn/hpc_norepl/home/rbro ...
written 8 hours ago by
rbronste • 200
• updated
7 hours ago by
Vijay Lakhujani ♦ 3.2k
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... I was wondering about a good method to compare read depth at specific positions (bed file intervals) between two bam files and get as an output the depth across both bam files next to each interval in question? Thanks! ...
written 14 hours ago by
rbronste • 200
• updated
13 hours ago by
Pierre Lindenbaum ♦ 114k
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... Kind of a straightforward question, but what is a quick/simple method to take a bed file with an avg bp size of 350 and extend every interval by 325bp in each direction? Thanks! ...
written 1 day ago by
rbronste • 200
• updated
1 day ago by
Alex Reynolds ♦ 26k
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... I was wondering whether there was a way to see the total number of genes that make up every panther pathway category? Just wondering about relative enrichment and if its just an artifact of vastly different numbers of genes that comprise every category? Thanks! ...
written 1 day ago by
rbronste • 200
• updated
1 day ago by
c.chakraborty • 100
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... Just thinking about different ways one could visually represent motif enrichment in target peak set over control, with significant points on the plot being marked with motif PWMs, if anyone can point me to a publication or some interesting code it would be much appreciated. Thank you! ...
written 5 days ago by
rbronste • 200
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... Perfect, thanks! Second option is what I am looking for in this instance. ...
written 5 days ago by
rbronste • 200
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Comment:
C: Parsing AME tsv file
... Ok figured it out seems to work like this for true positive intervals with specific motifs IDs:
grep -v ^motif sequences.tsv | grep -w tp | grep -w MA0258.2 | cut -f 2,3,6 | cut -d '_' -f 1 | tr ":-" "\t" | head
MA0258.2 chr12 15566967 15567317 tp
MA0258.2 chr11 88155633 88155983 tp
...
written 5 days ago by
rbronste • 200
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Comment:
C: Parsing AME tsv file
... Maybe a hint? :) Not as familiar with awk, though trying to learn. ...
written 5 days ago by
rbronste • 200
1
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... Actually GREAT now has an R package associated with it, which I find much more useful than the web interface.
[https://bioconductor.org/packages/release/bioc/html/rGREAT.html][1]
...
written 5 days ago by
rbronste • 200
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... I guess I can also take the aggregate bed files representing all chromosomes before downsampling and simply subsample intervals of 350bp in length and thereafter use your approach at the start of this thread to subsample those evenly across all chromosomes? Is there an easy way of taking just a BED ...
written 5 days ago by
rbronste • 200
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