@team.bank gtf hg38 pour featureCounts de subread

IFB Core Cluster Demande de logiciel ou de banque de données
1

Bonjour,
j'aurais besoin d'un GTF hg38 pour featureCounts
http://bioinf.wehi.edu.au/featureCounts/
La dernière version de Gencode serait parfaite. https://www.gencodegenes.org/human/
Merci d'avance
Magali

2

Bonjour
si vous voulez ajouter ce GTF aux banques communes, vous pouvez le récupérer sur mon projet
/shared/projects/lxactko_analyse/RASflow/gtf/gencode.v34.annotation.gtf
Il a été obtenu ainsi:

[mhennion@clust-slurm-client gtf]$ wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz
--2020-05-26 13:48:53--  ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz
           => ‘gencode.v34.annotation.gtf.gz’
Resolving ftp.ebi.ac.uk (ftp.ebi.ac.uk)... 193.62.197.74
Connecting to ftp.ebi.ac.uk (ftp.ebi.ac.uk)|193.62.197.74|:21... connected.
Logging in as anonymous ... Logged in!
==> SYST ... done.    ==> PWD ... done.
==> TYPE I ... done.  ==> CWD (1) /pub/databases/gencode/Gencode_human/release_34 ... done.
==> SIZE gencode.v34.annotation.gtf.gz ... 43164654
==> PASV ... done.    ==> RETR gencode.v34.annotation.gtf.gz ... done.
Length: 43164654 (41M) (unauthoritative)

100%[===================================================================>] 43 164 654  36,4MB/s   in 1,1s   

2020-05-26 13:48:54 (36,4 MB/s) - ‘gencode.v34.annotation.gtf.gz’ saved [43164654]

[mhennion@clust-slurm-client gtf]$ gunzip -d gencode.v34.annotation.gtf.gz 
[mhennion@clust-slurm-client gtf]$ head gencode.v34.annotation.gtf 
##description: evidence-based annotation of the human genome (GRCh38), version 34 (Ensembl 100)
##provider: GENCODE
##contact: gencode-help@ebi.ac.uk
##format: gtf
##date: 2020-03-24

Merci