New answers tagged bam
1
The best thing would be to figure out how to do this in UMItools. I don't know that tool at all, but it seems that it is supposed to be able to deal with / tag both reads in paired data. e.g. did you use --paired flag, etc.
I would suggest investigating that route first before you look at the next part of my answer.
Per Devon Ryan's comment suggestion I ...
1
When it comes to filter by a list, this is my favourite (much faster than grep):
# given a bam file "aln.bam" and a list of read names "reads.txt":
samtools view -h aln.bam \
| awk 'FNR==NR {reads[$1];next} /^@/||($1 in reads)' reads.txt - \
| samtools view -b - > filtered_aln.bam
Basically, the awk command first parses the reads.txt ...
3
It strongly depends on exactly what your protocol is. Note that there are a good number of tools for QCing capture data (here, here).
Off-target reads are a standard observation in capture experiments; recall that it is target enrichment, not target perfect purification, as commenter swbarnes2 suggests.
The real question is whether the proportion of those ...
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