2 votes
Accepted

gffread: GFaSeqGet errors on coordinate overhang

Basically, the source of the problem is issues with hard/soft clipped bases in short-reads RNAseq reads alignments to reference genome in post-transcriptome assembly steps. Truncating the ...
  • 2,656
2 votes

Hard-clip primers in a bam file

Another option would be to adjust the quality of the primer bases to be below the threshold that your variant caller uses. In my case I have "masked" the primer bases by dropping the quality to 0. ...
  • 2,576
1 vote

Precisely clipping bam file to bed coordinates

For single-end reads, generically: $ bam2bed < reads.bam > reads.bed $ bedmap --echo --fraction-ref 1 reads.bed roi.bed > answer.bed The BED file ...
1 vote

Precisely clipping bam file to bed coordinates

I am curious whether your pileup visualization tool is respecting the clipping. It is possible that there is a subtlety of samtools ampliconclip that your visualization is not understanding, with ...
1 vote

Hard-clip primers in a bam file

I know that the primer sequences are part of the genome and a variant there is no less valid than a variant anywhere else, You won't see variants under PCR primers. You get the primer sequence ...
  • 1,722

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