Question: How does featurecounts deal with the output from Bowtie?
0
gravatar for wangdp123
9 weeks ago by
wangdp123250
Oxford
wangdp123250 wrote:

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

bowtie rna-seq featurecounts • 141 views
ADD COMMENTlink modified 9 weeks ago by swbarnes29.2k • written 9 weeks ago by wangdp123250
0
gravatar for swbarnes2
9 weeks ago by
swbarnes29.2k
United States
swbarnes29.2k wrote:

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

ADD COMMENTlink written 9 weeks ago by swbarnes29.2k

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

ADD REPLYlink written 9 weeks ago by wangdp123250
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