miRNA-seq / Convert genomic BAM file to edgeR input format

Description

his tool takes BAM files as an input, calculates the number of times each sequence tag is identified and removes the ones for which the count is under the user defined threshold.

Parameters

Details

The tool takes as input a BAM file with sequence reads that have been aligned to a reference genome, so that genomic location information for each mapped sequence is available. Depending on how the 'Merge overlapping reads' parameter is set the counts are calculated so that only perfectly identical reads are summed up or all the reads that start and/or end at a certain genomic position are added together. The latter option is set by default since it greatly reduces redundancy in the counts data.

Output

edgeR-input.tsv: A text file with counts for each genomic feature, together with chromosome location info, suitable as input for tools like edgeR or DESeq.

References