Hi all,

I was trying to use HTSeq-qa to analyze the quality of my read alignments in my sorted bam file from samtools after HiSat2 mapping but am unable to proceed due to an error:

ValueError: 'count array' too small for sequence. 

I tested htseq-qa with other runs that worked before and they worked perfectly fine. I have tried searching up on what this error meant but to no avail. What could be the reason behind this error?

Also, is it advisable to run Ribo-Seq fastq files down the same pipeline as for RNA-Seq? Based on what I have read, Ribo-Seq is just the quantification of transcriptomic footprints and the sequencing is similar to RNA-Seq. Please do correct me if I am wrong here..

Any input is greatly appreciated, thank you!