I have a long list of read IDs of interest to me in a file called read_names.txt. it is simply in the format:
m54197_180831_211346/4981510/ccs m54197_180831_211346/6226723/ccs m54197_180831_211346/6619607/ccs ...
etc where these are the actual read names from a fastq file. I am then trying to find those in a bam file for which the fastq has been mapped, and I can accomplish this like:
for ID in `cat read_names.txt` do samtools view inbam.bam | grep $ID >> read_locs.sam done
However, this method is obscenely slow because it is rerunning samtools view for every ID iteration (several hours now for 600 read IDs), and I was hoping to do this for several
I tried sort of flipping the script a bit and running samtools view first but it only returned the first read ID present in the file and stopped:
samtools view inbam.bam | for ID in `cat read_names.txt`; do grep $ID >> read_locs.txt; done
Am I missing something or is this the only way to accomplish this task?