I have 2 BAMs of the some reads, but mapped to different genome. I extracted MAPQ from both, and get some index which correspond to reads that have the same MAPQ in both BAMs (using R). Then I can export those index in txt format.
Now how do I use the index found, for example, 2,3,4,5,8,9, to subset one of the BAM file?
The real problem is a bit more complex, as there are more than 2 BAMs, and I need to summarize the MAPQ across them.
Many thanks!
1 answer
Found a solution here (https://bioinformatics.stackexchange.com/questions/3380/how-to-subset-a-bam-by-a-list-of-qnames): samtools view file.bam | grep -f 'qnames.txt > subset.sam
The frustrated thing is, it seems that after filtering the BAM, in 10X, you have to convert it back to fastq then rerun the analysis.
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