Why do I have more reads in my .bam file than in my .fastq input file?
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3.3 years ago
francois ▴ 30

I seem to have more reads after alignment than before.

Before alignment

awk '{s++}END{print s/4}' reads.fastq

153265

After alignment

samtools flagstat align.bam

180051 + 0 in total (QC-passed reads + QC-failed reads)

0 + 0 secondary

26786 + 0 supplementary

0 + 0 duplicates

171567 + 0 mapped (95.29% : N/A)

[...]

I do not understand how can that be.

Can you help?

alignment bam fastq • 2.3k views
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Please post entire log from flagstat @op

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Had the same question couple of years ago!

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4
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3.3 years ago

the bam contains the supplementary (part of the read that maps elsewhere) + secondary (some other probable hits for the read) alignments

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