Entering edit mode
10 weeks ago
Pegasus ▴ 80
Using Linux, I successfully aligned my rna-seq data using Hisat2, converted sam to bam files, sorted them using samtools, and include these bam files with gtf.file in stringtie command line.
However, I got this "Error: no valid ID found for GFF record"
I consulted a previous post; stringtie Error: input file cannot be found
But I am still facing the same problem.
Here is the head -10 result;
Could you post the output instead of a screenshot? There seems to be an empty line there. Could you try to read the file with
Thank you barslmn,
I checked both gff.file and gtf.file for the same RG using gffread as below;
gtf using gffread
no valid ID found for GFF record
gtf using head -10
Both files did not show a similar pattern to the one posted in the GFF utilities;
Following the thread,
StringTIe Error: no valid ID found for GFF record
I believe Stringtie could not read my gtf.file (because gffread couldn't read it), maybe there is a problem in the trancript_ID, and gene_ID, so I still need recommendations ( which is the right command line to fix it)
Could you try to create your annotation file from the table browser? https://genome.ucsc.edu/cgi-bin/hgTables
It is a bacterial genome, which I believe is not supported by this website. I just updated the previous thread (gffread could not read my gtf.file)