Question: IGV - identification of sequencing errors
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gravatar for yasminsoareslima
18 months ago by
yasminsoareslima10 wrote:

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 enter image description here

Thank you!!

sequencing snp • 307 views
ADD COMMENTlink modified 18 months ago • written 18 months ago by yasminsoareslima10

how did you call the SNV ? are you showing the clipped bases in IGV ?

ADD REPLYlink written 18 months ago by Pierre Lindenbaum131k

the calling was performed by Somatic variant caller, from Illumina.
What are clipped bases?

Primers and adaptors were supposed removed. Thank you

ADD REPLYlink written 18 months ago by yasminsoareslima10

What are soft clipped reads??

ADD REPLYlink written 18 months ago by Pierre Lindenbaum131k

If it's amplicon based, then did you do anything to remove the primer sequences? Where should those be?

ADD REPLYlink written 18 months ago by WouterDeCoster44k

Yeah, they were supposed removed.

ADD REPLYlink written 18 months ago by yasminsoareslima10

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

ADD REPLYlink written 18 months ago by finswimmer13k
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