Hello all, I am having trouble getting StringTie or htseq-count to quantify my reads. I have some paired end RNA-seq data on human cells stored in fastq format. I ran the data through HISAT2 inputing my forward and reverse read files and using the built-in genome: [Human (homo sapiens) (b37): hg19]. I was successfully able to get BAM files and view the data in IGV to see my results. Now I would like to quantify my reads and when I run htseq-count I get the error message: An error occurred with this dataset:
Fatal error: Unknown error occured 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed. 400000 GFF lines processed. 500000 GFF lines processed. 600000 GFF lines processed. 700000 GFF lines processed. 800000 GFF lines processed"
I have tried using multiple different .GTF files through the UCSC main table and also under shared data libraries (hg19.GTF).
Thinking I was potentially using different genomes from alignment in HISAT2 and counting in htseq, I proceeded to import genomes from UCSC's browser in both .GTF and .FASTA formats so I could eliminate the possibility that I was just using a different genome for alignment and read counting.
Thanks in advance, Cheers