Question: Why do I have more reads in my .bam file than in my .fastq input file?
0
gravatar for francois
2.4 years ago by
francois10
francois10 wrote:

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?

bam alignment fastq • 1.7k views
ADD COMMENTlink modified 2.4 years ago by Pierre Lindenbaum131k • written 2.4 years ago by francois10

Please post entire log from flagstat @op

ADD REPLYlink written 2.4 years ago by cpad011214k

Had the same question couple of years ago!

ADD REPLYlink written 2.4 years ago by lakhujanivijay5.3k
4
gravatar for Pierre Lindenbaum
2.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

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

ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Pierre Lindenbaum131k
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