search

chess-genome / chess

Comprehensive Human Expressed SequenceS
http://ccb.jhu.edu/chess/
GNU General Public License v3.0
15 stars 2 forks source link

Making the GFF files compatible with hisat2_extract_splice_sites.py script #1

Closed foisys closed 3 months ago

foisys commented 5 years ago

Hi,

Trying to build splice sites and exon files for HISAT2 using the hisat2_extract_splice_sites.py script and chess2.1_assembly.gff file (transformed into GTF format via Bioconductor's rtracklayer library) but I am getting nothing... No output, big nada :-(

Any cue on fixing this situation?

Thanks in advance

S. Foisy, Ph. D. Project manager, bioinformatics Inflammgen lab Montreal Heart Institute

alevar commented 5 years ago

Dr. Foisy,

I was able to extract splice sites from chess2.1_assembly.gff by converting the annotation to GTF via gffread. Can you try using the following command: gffread chess2.1_assembly.gff -T -o chess2.1_assembly.gtf to perform the conversion. In case the gffread utility was not installed on your system alongside hisat2 and other tools, you can get binaries at http://ccb.jhu.edu/software/stringtie/gff.shtml

Please let us know if the solution worked and is acceptable.

Ales Varabyou

foisys commented 5 years ago

Hi,

Certainly will give a try; I’ll put a note that GTF from rtracklayer might not be the best…

Back to you asap.

S

Le 5 déc. 2018 à 17:28, Ales Varabyou <notifications@github.com mailto:notifications@github.com> a écrit :

Dr. Foisy,

I was able to extract splice sites from chess2.1_assembly.gff by converting the annotation to GTF via gffread. Can you try using the following command: gffread chess2.1_assembly.gff -T -o chess2.1_assembly.gtf to perform the conversion. In case the gffread utility was not installed on your system alongside hisat2 and other tools, you can get binaries at http://ccb.jhu.edu/software/stringtie/gff.shtml http://ccb.jhu.edu/software/stringtie/gff.shtml Please let us know if the solution worked and is acceptable.

Ales Varabyou

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/chess-genome/chess/issues/1#issuecomment-444675967, or mute the thread https://github.com/notifications/unsubscribe-auth/AD3vq6Dg1xY2oAjVDePSGlF3Uv5cRLnnks5u2Eh7gaJpZM4ZFGMT.

============================================================== Sylvain Foisy, Ph. D. Chargé de projet | Project Manager Bioinformatics Labo. de génétique et médecine génomique de l'inflammation Centre de recherche Institut de cardiologie de Montréal 5000 Bélanger Est Montréal, Qc H1T 1C8 CANADA

T: (514) 376-3330 x.2299 F: 514-593-2539 M: sylvain.foisy@inflammgen.org mailto:sylvain.foisy@inflammgen.org W: http://inflammgen.org http://inflammgen.org/