how to find a read by name in a bam file
hello
I am using cmpbam to compare bam files.For this I have to extract read names from original bamfile by using this command.
samtools view file1.bam K01:2179-2179 | cut -d ' ' -f 1 | sort | uniq > names.txt
Can someone help me that how I can find read id from my original bam file as k01:2179-2179 as shown in example.
Please help me to find this id from my original bam file.
Thank you
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Is that command not putting read id's in file called
names.txt?I believe the OP is trying to find and extract reads by name from a BAM file
What is
cmpbam? I can't find this tool.Most likely @Pierre's software.
not this one. But picard http://broadinstitute.github.io/picard/command-line-overview.html FilterSamReads with
READ_LIST_FILE=read_names.txtThis will output the line in the bam file with the "K01:2179-2179" read name in it, thus giving you the sequence of that read. (Is that what you're looking for?) Remove the
-m 1option if there is more than one read in the file expected to match the "K01:2179-2179" string. The-m 1makes it stop after the first find.That is not the read name. It is the
chromosome:start-stopinterval for which the OP wants to retrieve the reads (or just names). We are speculating until OP chooses to respond to comments in this post.Thanks for the clarification.