This is my first time aligning scRNA-seq reads to a reference genome to analyze differential gene expression. I am using htseq-count to obtain count files for my different samples and I am receiving the following error:
Error occured when processing input (record #1507153 in file SRR6350437_STAR_Aligned.sortedByCoord.out.bam): start too small [Exception type: IndexError, raised in _HTSeq.pyx:376]
I can not seem to find anything online explaining this error...
This is the command I ran for htseq-count:
htseq-count -s no -r pos -f bam SRR6350437_STAR_Aligned.sortedByCoord.out.bam /Desktop/OFD_scRNAseq/Homo_sapiens.GRCh38.104.chr_patch_hapl_scaff.gtf > SRR6350437_counts.txt
Any help is greatly appreciated!