How does featurecounts deal with the output from Bowtie?

Question

[wangdp123]

Hi there,

If the following command line is used to generate the SAM file.

bowtie -q -v 0 -k 10 -S -t <index.name> <input.fastq> <out.sam>

featureCounts program will be used to count the reads by enabling the multi-mapping reads counting:

featureCounts -t miRNA -g Name -O -M -a <mirbasefile> -o <outfile> <samfiles>

I wonder how featureCounts with the tags such as -O and -M will hand this situation as we know that this SAM file doesn't have "NH" tag? Will the command line above work properly for the microRNA quantification?

Many thanks,

Tom

Answer 1

[swbarnes2]

What is this for? Bowtie is not splice aware, it's not appropriate for RNASeq.

[wangdp123]

This is for microRNA analysis. There should be no need for splice aware.