uio-cels / solbakken_tlrs

Repository for Solbakken et al: Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions (Scientific reports)

Solbakken_TLRs

This repository contains all data used to generate the results in Solbakken et al: "Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions" published in Scientific Reports 29th of April 2016. DOI: 10.1038/srep25211. ENA archive: ERP013973 RNA sequencing of the spleen / headkindey of 6 juvenile Atlantic cod (Gadus morhua) individuals.

solbakken_tlrs's Issues

Confirm that use of BLAST's `-max_target_seqs` is intentional

Hi there,

This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's -max_target_seqs parameter:

• gene_searches/blast_commands

Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, there is a strong chance that this parameter is misused in your repository.

If the use of this parameter was intentional, please feel free to ignore and close this issue but I would highly recommend to add a comment to your source code to notify others about this use case. If this is a duplicate issue, please accept my apologies for the redundancy as this simple automation is not smart enough to identify such issues.

Thank you!
-- Arman (armish/blast-patrol)

Split fas_and_ML files

In https://github.com/uio-cels/Solbakken_TLRs/tree/master/selection_analysis, why not create separate files for the fasta part and the tree file? Then the reader can pick one of them and start working immediately, without having to extract the information she/he needs...