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Where to check out the alignment results for BWA

I used to use Bowtie2 and it gives the results

"Out of xxxxxxxxx reads, yyyyyyyy have been aligned 0 times, zzzzzz have been aligned exactly once....."

I just tried out the BWA but didn't see the counterpart. I wonder if there's any so I can compare.

Many thanks.

Field

bwa alignment
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written by field654 • field654

1 answer

Every aligner will output alignment stats in different ways so you can't get the same output in all cases. You can use a separate program like QualiMap (LINK), samtools idxstats etc to get comparative output from different alignments.

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written by GenoMax GenoMax

Thank you so much for getting back to me, Genomax. I will try out.

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written by field654 • field654

Hi Genomax,

The QualiMap worked for me fine. Thanks a lot. I have an additional question. Regarding the QC reports, I have duplicatioin rates from both my samples (WES, 13GB data each) of around 50%. I wonder if that's to be expected or too high.

Best, Field

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written by field654 • field654

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