Question: why my WGS bam file (after alignment) shows more reads than the starting fastq file
gravatar for maria2019
5 months ago by
maria201990 wrote:

I have one paired ended (150x2) WGS fastq file.

fastqc QC total read = ~ 459 M

fastqc QC after trimming total reads = ~ 458 M

after the alignment with bwa-mem and realigning around the indel, I used QUALIMAP for QC and the report shows ~723 M reads!

Why do I get more reads after the alignment?

fastqc qc qualimap wgs total read • 277 views
ADD COMMENTlink modified 5 months ago • written 5 months ago by maria201990
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