How to identify the miRNA counts column?

Question

[Shahzad]

I have miRNA data of a plant. I aligned the reads using Bowtie (short read aligner) against miRbase database miRNAs. Then I used samtools -> bamtools -> bedtools to get the counts. Now I have counts imported into R but I am confused which column contains the counts. Please help to name all the variables in count file.

Thank You.

[GenoMax]

What program from bedtools did you use?

In general you would want to use featureCounts or HTSeq-count to get your read counts from aligned BAM files.

[Shahzad]

I used "multicov" from bedtools.

[GenoMax]

I suggest that you use featureCounts instead. You can provide multiple bam files to featureCount. This will generate a matrix of counts that will have genes as rows and each sample as a new column.