Identify SNPs in C.virginica adult gonad RNAseq data

[kubu4]

Sample-specific sorted BAM files can be found in each sample-specific subdirectory here:

https://gannet.fish.washington.edu/Atumefaciens/20210726_cvir_stringtie_GCF_002022765.2_isoforms/

There's also a corresponding MD5 checksum file (use this confirm successful transfer of any files) in each sample-specific subdirectory.

Notebook detailing their creation is here:

https://robertslab.github.io/sams-notebook/2021/07/26/Transcript-Identification-and-Quantification-C.virginia-RNAseq-With-NCBI-Genome-GCF_002022765.2-Using-StringTie-on-Mox.html

NOTE: If downloading via wget, you'll need to use the --no-check-certificate option.

[kubu4]

For anyone tackling this, I should also note that the read group sample name (@RG-SM) tag has not been set in any of the samples! I'll try to get that info added this week.

Of course, if you're motivated, you can add that info yourself using samtools:

http://www.htslib.org/doc/samtools-addreplacerg.html

And, here's the metadata for each sample:

https://github.com/epigeneticstoocean/2018_L18-adult-methylation/blob/main/data/adult-meta.csv

EDITED: Clarified RG sample name, not just RG tag.