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The FASTA file need to have the same chromosome names as the GTF, i.e. chr1, chr2 etc. |
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I run STAR using this command line
!STAR --runMode genomeGenerate --genomeFastaFiles /content/drive/MyDrive/ncbi-genomes-2022-11-28/GRCh38_Cerrected.fna --sjdbGTFfile /content/drive/MyDrive/gencode.v34.annotation.gtfand this message shows up :
Fatal INPUT FILE error, no valid exon lines in the GTF file: /content/drive/MyDrive/gencode.v34.annotation.gtf
Solution: check the formatting of the GTF file. One likely cause is the difference in chromosome naming between GTF and FASTA file.
I tried to change chromosome names in the FASTA file format so they become chr instead of chromosome and still get this message, am I doing somethig wrong ?
description in fasta file : NC_000001.11 Homo sapiens chr1 GRCh38 Primary Assembly 248956422
GTF files : chr1\tHAVANA\ttranscript\t2560554\t2563504\t....
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