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urol-e5 / deep-dive-expression

Analyzing gene expression and gene/ncRNA coexpression in three species of stony coral. This work builds on completed summary of the ncRNA landscape of these species (deep-dive).
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GTFs for Peve and Ptua? #12

Open sr320 opened 1 day ago

sr320 commented 1 day ago

I am working on Hisat alignments and looking for gtfs for Peve and Ptua - to go here https://github.com/urol-e5/deep-dive-expression/wiki/Genomic-Resources

kubu4 commented 1 day ago

For Peve, I'll see what I can do. The GFF provided for that species is not really a GFF, as it's really only mRNAs and CDS. No exon or gene features...

$ awk '{print $3}' Porites_evermanni_v1.annot.gff | sort -u 

CDS
mRNA
UTR

This was a known issue when we started in deep-dive.

I think Ptua (this is the same as Pmea, right?) is very similar, but I have to do a bit more sleuthing into the backstory for this one.

sr320 commented 1 day ago

Sorry I thought you had aligned time series data

On Tue, Oct 15, 2024 at 11:02 PM kubu4 @.***> wrote:

For Peve, I'll see what I can do. The GFF provided for that species is not really a GFF, as it's really only mRNAs and CDS. No exon or gene features...

$ awk '{print $3}' Porites_evermanni_v1.annot.gff | sort -u

CDS mRNA UTR

This was a known issue when we started in deep-dive.

I think Ptua (this is the same as Pmea, right?) is very similar, but I have to do a bit more sleuthing into the backstory for this one.

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kubu4 commented 1 day ago

Only for Apul.

kubu4 commented 1 day ago

Okay, I think the Ptua GFF is actually more of a GTF, as there aren't any gene or mRNA features...

$ awk '{print $3}' Pocillopora_meandrina_HIv1.genes.gff3 | sort -u

CDS
exon
transcript

I can't remember what this means for alignments where a GFF is required. Maybe a GFF can be wrangled by changing transcript to gene and CDS to mRNA? I can't fully recollect if I ever did anything about this problem, but I'll keep rooting around my notebook to see what I can find.