RNAseq Feature Count Alignment Balb/c

Question

[ammasakshay]

I am having trouble with an alignment for an experiment involving Balb/c mice.

Specifically, in annotation during Feature Count.

This is the reference genome I am using for my sample: https://www.ncbi.nlm.nih.gov/assembly/GCA_001632525.1/ I am unable to find the annotation GTF file needed to proceed. How does one obtain this from the reference genome?

Thank you

[GenoMax]

No idea if this works. Try it out if you want and let us know: https://hackmd.io/@astrobiomike/conv-gb-to-gtf

There is a gbff file for Balb/c here: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/001/632/525/GCA_001632525.1_BALB_cJ_v1/GCA_001632525.1_BALB_cJ_v1_genomic.gbff.gz

[ammasakshay]

Tried, this already, doesn't work.

[Matthias Zepper]

The most up-to-date source is likely Ensembl Biomart - choosing the "Mouse strains" dataset. You can download all the required attributes as CSV/TSV, but will need to do a bit of perl/awk reshaping to get a gff file out of it. Alternatively, use the biomarRt/GenomicFeatures packages in R to output a gtf/gff.

If that sounds like too much hassle, you can export a few years old data from the Genome Browsers: There is a track hub for the UCSC Genome Browser and also an assembly in the Ensembl browser.. Both browsers can (usually) export gtf files.