Questions tagged [base-clipping]

The removal of bases at the end of reads to make an alignment better.

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1 vote
2 answers

Precisely clipping bam file to bed coordinates

I have a bed file of coordinates and would like to clip anything outside these regions in my aligned bam files. However, trying programs such as bedtools intersect and samtools ampliconclip (on ...
2 votes
2 answers

Hard-clip primers in a bam file

I am working on a sample which was sequenced using an amplicon kit and I would like to ensure that no variants are called in the PCR primer sequences. I know that the primer sequences are part of the ...
3 votes
1 answer

gffread: GFaSeqGet errors on coordinate overhang

Disclaimer: I had this issue posted on Tuxedo Tools users group and shared it on Twitter, but could not get an answer to this from the developers, nor find documentation of this issue online. So, I'll ...