Hi everyone,
I am using the latest version of GSNAP to get alignments for 29 RNAseq samples. So after I get a SAM alignment from GSNAP, I use samtools to convert it into BAM and then:
My GTF file contains only protein coding & lincRNAs and it is the latest version. I get the following error after running htseq-count command:
I have successfully run around 15 samples but I am getting this error in the other 14 samples. How can I solve this issue?
I am using the latest version of GSNAP to get alignments for 29 RNAseq samples. So after I get a SAM alignment from GSNAP, I use samtools to convert it into BAM and then:
samtools fixmate input.bam input_unsortfix.bam
samtools view -f 0x0002 input_unsortfix.bam | htseq-count -s reverse - Homo_sapiens.GRCh37.73.protein_linc.gtf > input.counts
Error: 'itertools.chain' object has no attribute 'get_line_number_string'[Exception type: AttributeError, raised in count.py:201]
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