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datngu / Circall

Circall is a novel method to discover circular RNA from paired-end RNA sequencing data
GNU General Public License v3.0
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mm10 / 11? #1

Open AMChalkie opened 1 year ago

AMChalkie commented 1 year ago

Hi,

Any plans to add mouse annotation objects to the release?

Cheers Alistair

datngu commented 1 year ago

Hi Alistair,

We currently don't have any plans to add mouse annotations to the releases. In general, Circall can work with Ensembl annotations, and you can follow our instructions https://github.com/datngu/Circall#31-prepare-bsj-reference-database-and-sqlite-annotation-file to generate the needed annotations.

In case you are still in trouble with the annotation, I am willing to help!

Best wishes, Dat

AMChalkie commented 1 year ago

No worries, example links for mouse mm10 are:

wget http://ftp.ensembl.org/pub/release-102/gtf/mus_musculus/Mus_musculus.GRCm38.102.gtf.gz gunzip Mus_musculus.GRCm38.102.gtf.gz

wget http://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz gunzip Mus_musculus.GRCm38.102.dna.primary_assembly.fa.gz

wget http://ftp.ensembl.org/pub/release-102/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz gunzip Mus_musculus.GRCm38.cdna.all.fa.gz