I would like to count rnaseq mapped reads on a bacterial genome. Firstly I aligned the reads using bbmap with the command: bbmap.sh ref=P_riograndensis_LN831776.fas in=A1_trim.fastq out=A1_bbmap.sam
However, when I try to count the mapped reads with htseq (htseq-count -i locus_tag -t gene A1_bbmap.sam P_riograndensis_LN831776.gff), the following error occurs: "("Illegal CIGAR string '48='", 'line 5 of file A1_bbmap.sam')"
Here is the line 5 of A1_bbmap.sam. ASFH0:01510:12713 0 LN831776 LN831776 Paenibacillus riograndensis SBR5 genome assembly SBR5(T) ,chromosome : I. 81663 3 48= * 0 0 TGAGAAGCCGGAGCCGCAGCGAAAGCGAGTCTGAATAGGGCGACTGAG ??>;;6;<6<7@@<7<><>=<>=4<=><=<===?7><;;4;;<<;;;; XT:A:R NM:i:0 AM:i:3
I believe something is wrong with bbmap sam output. But I could not realize what is the problem. Maybe the "=" signal is not expected?