Hi,
I have BAM files from Mapsplice and I wanted to quantify the expression levels with HTSeq. But I received following error. Do you think it is regarding the aligner or what is the problem?
samtools view file.bam | htseq-count --stranded=no hg19/Annotation/Genes/genes.gtf > test.txt
Warning: Read file:8:2203:10838:61544/2 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted)
Error: 'itertools.chain' object has no attribute 'get_line_number_string'
[Exception type: AttributeError, raised in count.py:200]
Thanks in advance
I have BAM files from Mapsplice and I wanted to quantify the expression levels with HTSeq. But I received following error. Do you think it is regarding the aligner or what is the problem?
samtools view file.bam | htseq-count --stranded=no hg19/Annotation/Genes/genes.gtf > test.txt
Warning: Read file:8:2203:10838:61544/2 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted)
Error: 'itertools.chain' object has no attribute 'get_line_number_string'
[Exception type: AttributeError, raised in count.py:200]
Thanks in advance
Comment