Error "start too small" when running htseq-count on a sorted .bam file
0
0
Entering edit mode
6 weeks ago
elee228 • 0

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 • 183 views
ADD COMMENT
0
Entering edit mode

I'm not sure that a reference that includes haplotypes and patches is best for STAR:

(emphasis original)

Generally, patches and alternative haplotypes should not be included in the genome

https://physiology.med.cornell.edu/faculty/skrabanek/lab/angsd/lecture_notes/STARmanual.pdf

I'd start by looking at what record #1507153 looks like.

ADD REPLY

Login before adding your answer.

Traffic: 1558 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6