Question: PacBio reads mapping statistics abnormaly high
2
gravatar for alexis.groppi
4.8 years ago by
France/Bordeaux/University of Bordeaux
alexis.groppi30 wrote:

Hi,

I have used bwa mem 0.7.12 to map PacBio reads on a reference genome. Then I want to have some statistics on this mapping. When I count the total number of reads in the starting fastq file, the result is 250,000) I have used my favorite tool : Qualimap2.2 But in the result the number of total reads and mapped reads are abnormaly high : resp 612,000/598,000 I have tried also with samtools 1.3 (samtools flagstat). But the result is the same : the number of total reads and mapped reads are abnormaly high : resp 612,000/598,000

How explain this huge difference ?

Am I doing something wrong ?

Thanks for your help and expertise

Alexis

pacbio mapping • 1.5k views
ADD COMMENTlink modified 4.8 years ago by WouterDeCoster45k • written 4.8 years ago by alexis.groppi30
2

Check what happens to the reads that map to multiple places equally well. Sometimes aligner report all such alignments, then the number of mapped reads could be higher that the total number of reads. Also, are you aligning fastq files or raw PacBio files?

ADD REPLYlink written 4.8 years ago by Biomonika (Noolean)3.1k

Also I would recommend to subsample to small number of reads (e.g. 20), run mapping and look at the alignments manually.

ADD REPLYlink written 4.8 years ago by Biomonika (Noolean)3.1k

Good suggestion, I will try. Thanks !

ADD REPLYlink written 4.8 years ago by alexis.groppi30

Hi Noolean, I'm aligning fastq files

ADD REPLYlink written 4.8 years ago by alexis.groppi30
2
gravatar for WouterDeCoster
4.8 years ago by
Belgium
WouterDeCoster45k wrote:

I suspect reads mapping to repetitive elements.

ADD COMMENTlink written 4.8 years ago by WouterDeCoster45k
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