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Old 10-24-2016, 08:33 PM   #2
finswimmer
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Location: Europe

Join Date: Oct 2016
Posts: 60
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What do you mean by "I have both fastq and bam files"? Is this realated to your "several thousands of sequences" or your genome?

If it's the first than you already have a file were all your sequenced were tried to mappe to a reference (was this your genome?). You can use than use samtools to asked how many reads are mapped.

Code:
samtools view -F 0x4 -c mybamfile.bam
or

Code:
samtools flagstat mybyfile.bam
fin swimmer
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