Bamqc more mapped reads than total reads in dataset?

[Esther Kockelmans]

Hi,

I am a but confused about the Qualimap output.

My dataset consists of 12,606,144 reads. I have aligned these reads against two different assemblies.

Qualimap tells me that there are 13,488,573 (for assembly nr. 1) and 13,788,026 (for assembly nr. 2) reads in my dataset, which is incorrect.. I think Qualimap calculates the amount of reads by doing a line count on the sorted bam file, since this is similar to 13,488,573 and 13,788,026. But now I am a bit confused about the amount of "mapped reads". The amount of mapped reads is higher than the amount of reads I used for the alignment.. but how is that possible? Is this also fixed with the new Qualimap version?

Hope you can help me with this.

Kind regards,
Esther

[Konstantin Okonechnikov]

Hi,

Qualimap counts the read alignments, simply SAM records, therefore if there are multiple read alignments allowed or some permission to split the read into segments this could lead to higher amount read records. Which alignment tool was used and with what settings?  Probably this info could help to figure out what are the additional alignments. 

Best regards,

   Konstantin 

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[Esther Kockelmans]

Hi,

Thanks for the quick respond. This is the command I used for the alignment (using minimap2):

# align the (filtered) hifi reads of the blue shark against the filtered hifiasm assembly of the blue shark
/home/hsl_s1101570/software/minimap2-2.22_x64-linux/minimap2 -ax map-hifi --secondary=no \
/home/hsl_s1101570/data/hifiasm_output/assembly/bluesharkhifiasm_filtered.fa \
/home/hsl_s1101570/data/hifi_reads_fasta/*reads.bam.fa > /home/hsl_s1101570/data/alignment_blue_shark/alignment_bs_filtered.sam

In the command I specify the --secondary=no option so that means that no multiple read alignments are allowed right?

Kind regards,
Esther

Op vrijdag 4 februari 2022 om 16:01:50 UTC+1 schreef Konstantin Okonechnikov: