how to find a read by name in a bam file
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7.0 years ago

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

next-gen-sequencing • 10k views
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Is that command not putting read id's in file called names.txt?

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I believe the OP is trying to find and extract reads by name from a BAM file

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What is cmpbam? I can't find this tool.

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Most likely @Pierre's software.

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not this one. But picard http://broadinstitute.github.io/picard/command-line-overview.html FilterSamReads with READ_LIST_FILE=read_names.txt

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samtools view file1.bam | grep -m 1 K01:2179-2179

This 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 1 option if there is more than one read in the file expected to match the "K01:2179-2179" string. The -m 1 makes it stop after the first find.

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This will output the line in the bam file with the "K01:2179-2179" read name in it

That is not the read name. It is the chromosome:start-stop interval 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.

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Thanks for the clarification.

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