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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
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