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Old 03-09-2018, 04:51 AM   #1
Flock
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Location: Utrecht

Join Date: Jan 2018
Posts: 1
Question Keep in-frame reads only

Hi all,

I have been working with Ribosome Sequencing datasets over the past few months. My ultimate gole is to determine the codon that's in the P-site of the Ribosome Protected Fragements. These fragments are roughly 29-30 nt in length. The P-site is located at position 12 (= nts 13, 14, 15).

We've gotten pretty far: standard adapter trimming, contaminant removal and alignment to the reference genome. Because for 'translating' the codon in the P-site to an amino acid it is very important that the read is in-frame (the first three nucleotides code for an amino acid), I would like to filter out any non-aligned or ambigious-frame reads from the alignment output (BAM).

Output preferably in fastq format, since this is compatible with the tool we use to map the P-site codons to amino acids.

Does anyone know of a tool or a way to do this?

Thanks a lot!

All the best,

Flock

Last edited by Flock; 03-09-2018 at 07:12 AM.
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