User: yarmda

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yarmda0
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Posts by yarmda

<prev • 32 results • page 1 of 4 • next >
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Comment: C: How to extract only continuously aligned reads from a SAMfile
... The solution is listed as samtools view -f 256 Input.bam | awk '$6 ~/S/ && $7 == "=" {print $0}' > Secondary_clipped.sam But, this pulls out secondary alignments and then checks if there is a soft clipping event. Secondary alignments may happen, but this won't necessarily capture all c ...
written 4 weeks ago by yarmda0
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Comment: C: How to extract only continuously aligned reads from a SAMfile
... We are considering that option, but that still leaves a risk of chimeric reads being included, depending on how the trimming worked out. We're hoping to be able to identify about 30-40% of the reads as non-chimeric. If we can't identify even 15% as non-chimeric, we'll probably resort to trimming. ...
written 5 weeks ago by yarmda0
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How to extract only continuously aligned reads from a SAMfile
... We found that most of the reads in a large number of samples have been ligated together from various fragments. I am trying to see if I can identify and salvage those reads that managed to slip through the cracks and are whole/continuous. I can visualize the alignments and see large gaps among many ...
alignment samtools sam written 5 weeks ago by yarmda0
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Comment: C: bedtools: extracting no coverage regions
... Hi Aaron, I just want to bump one of the replies to this comment. I would also like to summarize coverage by region. Is that doable with bedtools? > This has worked very well, thank you! > I am now looking to calculate average coverage for my CDS features, one value per CDS, and I can't see ...
written 4 months ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... How does this work behind the scenes? I'm finding the order of the PL:DP:AD flags is reversed when the FILTER lists "PASS" compared to when it is "NOT_TARGET_ORGANISM_STRAIN" ...
written 4 months ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... This has been exceedingly helpful. Now, if I wanted to print the AD and the DP instead of the INFO column and instead of filtering on the AD - would that be possible? ...
written 4 months ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... I tried that to no success. Below I define the variable allele to be T, the same as the original expression. I have replaced "T" in getDisplayString().equals("T") with "$allele", but now everything is considered false. Have I made a mistake? allele="T" echo $allele java -jar dist/vcffi ...
written 4 months ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... Can you describe how to pass a shell variable to the javascript expression? ...
written 4 months ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... That's good thinking. I considered the loop, but hadn't realized how I could avoid loading the entire vcf each iteration. ...
written 4 months ago by yarmda0
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Comment: C: How best to parse samtools mpileup results?
... This looks really close to what I want. Is there a way I can feed the expression a file containing a series of positions with alleles of interest and a minimum AD? ...
written 4 months ago by yarmda0

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Supporter 4 weeks ago, voted at least 25 times.

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