This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Selection of GTF file from gencode

I'm attempting to use STAR to index the mouse genome. I'm using the following command:

/opt/conda/envs/STAR/bin/STAR --runMode genomeGenerate --runThreadN 8 --genomeChrBinNbits 12 --limitGenomeGenerateRAM 60000000000 --genomeDir /desktop/output/mouse_genome_index/ --genomeFastaFiles /desktop/mouse_input_data/mouse_gencode_transcripts.fa --sjdbGTFfile /desktop/mouse_input_data/mouse_gencode_annotation.gtf --genomeSAsparseD 3

I downloaded the mouse genome FASTA and GTF files from the GENCODE website : https://www.gencodegenes.org/mouse/ I used the following GTF file enter image description here

and this fasta file: enter image description here However, I encountered an error that I'm having trouble understanding:

Fatal INPUT FILE error, no valid exon lines in the GTF file: /desktop/mouse_input_data/mouse_gencode_annotation.gtf Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file.

it is related to the GTF file, but I don't know which GTF file I have to download from gencode in this case ( --sjdbGTFfile )

star
• 1,989 views • link
updated by GenoMax GenoMax • written by Nodilan • Nodilan

Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the code formatting option shown below)

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

One likely cause is the difference in chromosome naming between GTF and FASTA file.

did you check that ?

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

this is an example of line in my gtf file :

chr1 HAVANA gene 3143476 3144545 . + . gene_id "ENSMUSG00000102693.2"; gene_type "TEC"; gene_name "4933401J01Rik"; level 2; mgi_id "MGI:1918292"; havana_gene "OTTMUSG00000049935.1";

this is an example in my FASTA file having the same gene id

ENSMUST00000193812.2|ENSMUSG00000102693.2|OTTMUSG00000049935.1|OTTMUST00000127109.1|4933401J01Rik-201|4933401J01Rik|1070|TEC|

• 0 views • link
written by Nodilan • Nodilan

Fasta file should be the genomic sequence, not the sequence of the genes.

>chr1
ATCGTACGATGATCGTACGTAGCTAGTGAC....
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted.

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this