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RSEM is an app for counting the number of hits for each gene or transcript in a BAM file from a read to transcript mapping.
- To use RSEM 1.2.12, import your transcript file in fasta format, and your mapping file (reads to transcript file) in BAM format.
- Resources: http://deweylab.biostat.wisc.edu/rsem/
Use BAdehydxtrinity.sorted.6747.bam and Trinity.fasta 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.
- Default parameters , except check the box for paired reads.
Expect 2 files as output, RSEM.genes.results and RSEM.isoforms.results.