HISAT2 Error

Question

[SHXVRR]

I seem to keep running into problems. whenever I run this hisat2 command:

stringtie -p 8 -G hg38_tran/hg38_ucsc.annotated.gtf -o files/ERR2707360.gtf -l ERR2707360 files/ERR2707360.bam

It gives me:

chr1    hg38_refGene    stop_codon    67093580    67093582    0.000000    -    .    gene_id "NM_001276352"; transcript_id "NM_001276352";  gene_name "C1orf141";chr1    hg38_refGene    stop_codon    67093580    67093582    0.000000    -    .    gene_id "NM_001276352"; transcript_id "NM_001276352";  product "uncharacterized protein C1orf141 isoform 2";
Abort trap: 6

I am using the HISAT2 index file from their website: https://daehwankimlab.github.io/hisat2/download/

Im not sure how the formatting is wrong if I took it from the official site. Do I need to get another genome file and then restart the pipeline?

Answer 1

[ATpoint]

You're mixing up a lot here. First, you're not running hisat2 but a tool called stringtie meant to assemble RNA-seq data. Stringtie does not use hisat2 index. You use a GTF here, for reference-guided assembly. Output is a GTF file, which is exactly what you get. I see no problems here.

[SHXVRR]

Sorry, that's what I meant. This is a string tie function and hg38_ucsc.annotated.gtf is not a hisat2index but a normal gtf. When I switched the .gtf with an official human genome like: https://www.gencodegenes.org/human/release_38.html, It worked. Thanks for the clarification. Idk why I called it a hisat2 command when its stringtie