Extract aligned bases for each read from a large mapping data set
Hi
I have a large mapping dataset (about 170 million of reads in the alignment (sam file). I also have the input data (fasta.gz and fastq.gz files) I want to know how to efficiently extract next items using a single script from the sam file. I know samtools stats get some of them, however I would like to have one single script.
- Total reads
- Total bases
- total aligned reads
- total aligned bases
- total bases per read
- aligned bases per read
Thanks for any help
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adriana.gallego.02 •
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Are you sure you want that in a log? That would be 340 million lines right there!
You can use
Qualimap(LINK) as an option to get detailed stats for your alignments.