I run the code below
samtools view MT1/Tophat_Out/accepted_hits.sorted.bam | python -m HTSeq.scripts.count -q -s no - ~/Indexes/Mus_musculus/UCSC/mm10/Genes/genes.gtf > MT1/MT1.count.txt
Then I got this error: /bin/python: No module named HTSeq.scripts
I rerun the code and not sure what changed but I got a new error:
Error occurred when reading beginning of SAM/BAM file.
file has no sequences defined (mode='r') - is it SAM/BAM format? Consider opening with check_sq=False
[Exception type: ValueError, raised in libcalignmentfile.pyx:1000]
I found a solution on the Internet:
which said: "the script was added to ./local/bin instead of /bin"
However, I don't know how to apply in my case. Would you please help? Thank you so much!