How to identify the miRNA counts column?
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.
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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.
I used "multicov" from bedtools.
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.