HTseq: Error occured when reading beginning of SAM/BAM file.

Question

[maple964]

Dear all,

I tried to use HTseq for a week because I want to use "--nonunique" function. However

Error occured when reading beginning of SAM/BAM file.
  'pysam.csamtools.AlignedRead' object has no attribute 'reference_start'
  [Exception type: AttributeError, raised in _HTSeq.pyx:1371]

I tried to update the newest version of HTseq, and someone suggested to convert bam>sam>bam. I also tried, but it didn't work. (for this I also updated samtools 1.9 version)

I checked this page htseq-count: error when reading beginning of SAM/BAM file., but I couldn't find any solution.

This is my comment line

htseq-count -f bam -s no -m union --nonunique all -q accepted_hits_sam2bam.sorted /usr1/thhuang/index/TAIR10_GFF3_genes_transposons.gtf > Hiseq_count3.count

I am too new in bioinformatics. I really need some help.

Thank you all in advance

[GenoMax]

I wonder if this is applicable in your case: https://github.com/hall-lab/svtyper/issues/37

Side note: you can use -M option with featureCounts to count multi-mapping reads (caution: this is not a good idea for RNAseq data).