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