get the number of reads

Question

[Oliver]

how we can get the number of reads after mapping first I use bbmap follwed by bedtools intersect and thin i use bedtools coverage i have now file of cover.text

what is the command that i can use to get the number of reads thank you

[ATpoint]

Do you need a count matrix for RNA-seq differential analysis? If so, as I suggested in a previous question of yours, use a dedicated RNA-seq tool such as featureCounts. All you need is a BAM file and a GTF annotation file to get a count matrix which you then plug into the standard differential software pipelines. bedtools is an awesome suite of tools but for RNA-seq there are way faster alternatives which basically take care of everything so you get a ready-to-use output matrix. Especially if you're new to the field it is highly recommended to stick to established workflows to avoid unnecessary trouble. Please see https://www.bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html for some suggestions on how to obtain a count matrix from BAM files. I recommend going through this tutorial as it covers essentially all important aspects of standard analysis.

What is your final analysis goal?