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A tool for counting the number of reads that fall within the range of features defined in a GFF file.
- To use HTSeq-count 0.5.4, import your data in SAM and gff or gtf format.
- Resources: http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
Use testfile.sam and hy5_rep1_transcripts.gtf from the directory above as test input.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Use these parameters within the DE app interface:
- MODE - union
- feature type - exon
- feature attribute - gene_id
- default for the rest
Expect a tab delimited file as output. For the test case, the output file you will find in the example_data directory is named FeatureCounts.txt.