User: aalith

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aalith0
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Posts by aalith

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Comment: C: Finding # of UMIs with and without specific SNP
... Sorry for editing this so much, but having another bit of trouble.. To see the nucleotide at the specific point of interest, I did the following - subset to only chromosome 3 at position 50093871 (for reads in bamfile.fetch('3', 50093871, 50093872)) - Find the specific nucleotide by reads.seq[5009 ...
written 17 days ago by aalith0
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Comment: C: Finding # of UMIs with and without specific SNP
... So I'll have to use *fetch* instead of pileup so i can hold on to the tags? ...
written 17 days ago by aalith0
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Comment: C: Finding # of UMIs with and without specific SNP
... this is unbelievably helpful, thank you! ...
written 17 days ago by aalith0
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Comment: C: Finding # of UMIs with and without specific SNP
... Sorry for being unclear - I am trying to count the number of UMIs associated with reads that contain a particular SNP. So, count the number of different UMIs associated with reads that do and do not contain the SNP ...
written 17 days ago by aalith0
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Comment: C: Finding # of UMIs with and without specific SNP
... UMIs are currently denoted by the XM tag in my bam file ...
written 17 days ago by aalith0
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Finding # of UMIs with and without specific SNP
... I am trying to count the number of UMIs associated with reads that contain a particular SNP. So, count the number of different UMIs associated with reads that do and do not contain the SNP I was thinking of first parsing through the processed bam files to extract all reads at a specific site ...
rna-seq snp sequencing written 17 days ago by aalith0 • updated 17 days ago by i.sudbery5.2k
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Comment: C: Piped Commands, Picard to BWA
... Sorry if this doesn't fit into the site's focus. but the other thread hadn't answered why the piped command may not work. There's an error about not being able to write to dev/stdout for some reason. Is there any way around this besides using samtools? ...
written 5 weeks ago by aalith0
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(Closed) Piped Commands, Picard to BWA
... I'm new to NGS analysis and was wondering how to run a piped command to avoid reading and writing huge intermediate files. I only have a little experience with the linux commands, but I am running from inside a GATK docker image. Does the command line just look like... gatk RevertSam (stuff) ...
picard piped bwa written 5 weeks ago by aalith0
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Comment: C: Pipe SamToFastq, BWA mem not working
... Could abbysue's problem be due to the fact that it's running inside docker and not on the local machine? the piped command listed should work ...
written 5 weeks ago by aalith0
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Comment: C: Pipe SamToFastq, BWA mem not working
... I've read that the behavior of Picard in regressing to a fastq file is preferable (forum post on Biostars, have to find it real quick) ...
written 5 weeks ago by aalith0

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