How to address "*" as RNAME in SAM file

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2.5 years ago

Matej • 0

I'm making a program in java for alignment visulaization. The input is a ref genome and a sam file with the alignment. I'm using RNAME field in the SAM file to see to which sequence does the alingment belong to. How to address when there is "" instead of a RNAME. In my SAM file for Ecoli alignemnt all RNAME fields are "" so I've added into my code that if there is only one sequence in the referente genome file the program takes the sequence name from the header as RNAME. I don't know if this aproach is correct and I don't know what to do when the referente genome file has more than one sequence. Any advice/explanation would be appreciated.

bam alignment sam fasta sequence • 489 views

ADD COMMENT • link updated 2.5 years ago by Pierre Lindenbaum 164k • written 2.5 years ago by Matej • 0

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The input is a ref genome and a sam file with the alignment.

don't reinvent the wheel and use htsjdk. https://github.com/samtools/htsjdk/

ADD REPLY • link 2.5 years ago by Pierre Lindenbaum 164k

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