Entering edit mode
3.6 years ago
wangdp123
▴
340
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
This is for microRNA analysis. There should be no need for splice aware.