AnswerBun.com

RNASeq read coverage in protein space?

Bioinformatics Asked on December 23, 2021

  1. I used samtools depth to find the per base-pair read coverage over a number of isoform contigs from my Trinity assembly.
  2. I have also conducted a multiple sequence alignment of those isoforms using Clustal Omega DNA aligner.

In my final step, I want to assess the per-residue read coverage of the consensus amino acid sequence to demonstrate an idea of confidence in that sequence.

Does anyone have any tips on how to go about doing this and whether there are existing tools for such things?

One Answer

Answer from @cephbirk, converted from comment:

What I ended up doing was to choose the read coverage for the lowest covered nucleotide in each codon as each residue's read coverage.

Answered by gringer on December 23, 2021

Add your own answers!

Related Questions

Downloading SRA Files from AWS

1  Asked on December 6, 2020

       

NCT search in PubMed via Entrez (python)

0  Asked on December 5, 2020 by nutarelli-federico

       

using snakemake shadow rules to store temp files on local nodes

1  Asked on December 2, 2020 by kamil-s-jaron

 

Software for taxonomic assignment?

2  Asked on December 1, 2020

     

Detecting Allelic Imbalance

0  Asked on November 26, 2020 by krizbomb

   

Mapping statistics from bam file using bbtools and sambamba

2  Asked on November 25, 2020 by bioinfonext

         

Preprocessing Affymetrix SNP Array Matrix

0  Asked on November 17, 2020 by thanh-nguyen

 

Ask a Question

Get help from others!

© 2023 AnswerBun.com. All rights reserved. Sites we Love: PCI Database, MenuIva, UKBizDB, Menu Kuliner, Sharing RPP, SolveDir