IGVtools count
IGVtools count
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The "count" command computes average feature density over a specified window size across the genome. Common usages include computing coverage for alignment files and counting hits in Chip-seq experiments.
Quick Start
- To use IGVtools count, import your data in SAM, BAM, or BED format.
more info: http://www.broadinstitute.org/igv/book/export/html/72
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> htseq_count
Input File(s)
Use testfile.sam from the directory above as test input.
Parameters Used in App
- Default parameters only, no further configuration needed.
Tool Source for App