GRCh38_gencode_v44 primary annotation: CTAT source lib versus genecode DB download

[Mbandi Kimbung]

Hello CTAT users and Brian,

Thanks for this tool and the support.

I previously created a STAR index with the following:

https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/GRCh38.primary_assembly.genome.fa.gz

https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_44/gencode.v44.primary_assembly.annotation.gtf.gz

To make use of CTAT, I obtained:

https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/GRCh38_gencode_v44_CTAT_lib_Oct292023.source.tar.gz
tar -xvf GRCh38_gencode_v44_CTAT_lib_Oct292023.source.tar.gz

Could you clarify why the following are different:

diff ./GRCh38_gencode_v44_CTAT_lib_Oct292023.source/gencode.v44.annotation.gtf gencode.v44.primary_assembly.annotation.gtf

Kind regards,

Mbandi

[Brian Haas]

Hi,

Here's how the ctat genome lib modifies the gencode resources to better support fusion calling:

https://github.com/TrinityCTAT/ctat-genome-lib-builder/wiki/human_customized_genome_lib

best,

Brian

--
You received this message because you are subscribed to the Google Groups "Trinity_CTAT_users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinity_ctat_us...@googlegroups.com.
To view this discussion visit https://groups.google.com/d/msgid/trinity_ctat_users/035c1eb2-7f70-4223-98b0-cc0fe3734e11n%40googlegroups.com.

--

--
Brian J. Haas
The Broad Institute
http://broadinstitute.org/~bhaas