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HCGB-IGTP / XICRA

Small RNAseq pipeline for paired-end reads
MIT License
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Annotation file error when running biotype #20

Closed Ben7124 closed 3 years ago

Ben7124 commented 3 years ago

Hi Jose,

I downloaded the gtf annotation file from https://www.gencodegenes.org/human/ (the first link on that page) labelled gencode.v38.annotation.gtf. When I ran the biotype module, I got the following error. I assume that I need to download a different annotation file? Where can I get that? Thanks again!! -- Ben

Load annotation file gencode.v38.annotation.gtf ... ||

ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file. The specified gene identifier attribute is 'transcript_biotype' An example of attributes included in your GTF annotation is 'gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "proc essed_transcript"; transcript_name "DDX11L1-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:37102"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_tran script "OTTHUMT00000362751.1";' The program has to terminate.

Ben7124 commented 3 years ago

I am re-running it with the primary annotation. Let us see if that works!

JFsanchezherrero commented 3 years ago

Hi there,

I assume you fixed it right? It might be useful if you provide with the annotation file (link) that you use and worked for you. For future users and readers of this thread, basically.

Best regards,