Entering edit mode
5.0 years ago
yasminsoareslima
▴
10
Hi to all,
I've already read that Illumina reads mostly common present errors at the end.. however, never read about any issue at the beginning of them.
I have called SNVs at the beginning and end of my reads that I don't feel like trusting, although the mapping quality and phread quality appears to be of high quality.
What would you tell me? Does this look like an sequencing error?
obs: i cannot perform trimming because my library is amplicon-based
Print screen of my IGV overview. Its a T>C change, it appears in both strands, but as mentioned, in the end or beginning of the amplicon
Thank you!!
how did you call the SNV ? are you showing the clipped bases in IGV ?
the calling was performed by Somatic variant caller, from Illumina.
What are clipped bases?
Primers and adaptors were supposed removed. Thank you
What are soft clipped reads??
If it's amplicon based, then did you do anything to remove the primer sequences? Where should those be?
Yeah, they were supposed removed.
Hello,
could you show us the resulting line in your vcf file?
If this is paired end data: Use the "View as pairs" option if you right click in the alignment track. Do both directions of a read pair show this variant?
fin swimmer