Question: Why do I have more reads in my .bam file than in my .fastq input file?
0
gravatar for francois
18 months 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 • 948 views
ADD COMMENTlink modified 18 months ago by Pierre Lindenbaum125k • written 18 months ago by francois10

Please post entire log from flagstat @op

ADD REPLYlink written 18 months ago by cpad011212k

Had the same question couple of years ago!

ADD REPLYlink written 18 months ago by lakhujanivijay4.7k
2
gravatar for Pierre Lindenbaum
18 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum125k 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 18 months ago • written 18 months ago by Pierre Lindenbaum125k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 623 users visited in the last hour