Extract aligned bases for each read from a large mapping data set
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15 months ago

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

alignment • 285 views
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total bases per read
aligned bases per read

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.

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