New answers tagged

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 ...


Top 50 recent answers are included