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Error "start too small" when running htseq-count on a sorted .bam file

Hello,

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!

htseq-count htseq
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updated by swbarnes2 swbarnes2 • written by elee228 • elee228

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