Alignment: how to deal with read mapped on decoy
Hello all,
I made my alignments with a human reference containing decoys. I know how to remove reads that aligned up with decoys but what I don't know is: should I do it?
For the header it's the same thing, do I have to remove the @SQ lines corresponding to the decoys ?
I have some reads with the R1 on "normal" chromosome and R2 on decoy, it's usual to have this type of alignment?
Thanks a lot in advance 😀
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berick •
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quentin54520 •
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quentin54520 •
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What type of sequencing data is this, what is the goal of your analysis, and what software are you currently using?
It's whole genome sequencing from a cohort of patients. The goal is to identify the genetic causes of their rare disease ( SNV, short indel or SV). for the software: i used Bwa mem with the reference hg38 no_alt_plus_hs38d1_analysis_set.
trash them. you won't be able to annotate or to make any sense out of them till a new genome build which integrates them comes.