Hello,
I am working on deriving HRD scores for human geome samples.
As part of this, the quality report after adaptor triming showsa broad range in the reads length distribution. I am attaching the image here.
Do I require to filter the reads of specific length before proceeding for alignmnet with reference (or) is it good to proceed for alignmnet as is? I could see there is an intense length distribution below 150 bp and majority of the reads are around 150 bp. What I suspect is to filter the reads below 150 bp?
Please anyone give your thoughts.
Your inputs are greatly appreciated.
1 answer
It is normal to see a range of read lengths after adapter trimming, especially if you have short inserts in your libraries. You could try filtering the reads to be of a certain minimum length (we started next generation sequencing data with ~35 bp reads and those can still be reasonably aligned to human genome). Very short reads will tend to multi-map. You will need to decide what to do with those. Looks like you have millions of reads here so filtering out reads shorter than 50 bp may end up losing a relatively small percentage of data.
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