Galaxy |

RSEM prepare reference (version 1.1.17)

Reference transcript source:

reference fasta file:

The files should contain the sequences of transcripts.

Map of gene ids to transcript (isoform) ids:

Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character ) The map can be obtained from the UCSC table browser group: Genes and Gene Prediction Tracks table: knownIsoforms Without a map: If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file. Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.

reference name:

A one word name for this RSEM reference containing only letters, digits, and underscore characters

PolyA :

The length of the poly(A) tails to be added. (Default: 125):

Disable the conversion of 'N' characters to 'G' characters in the reference sequences:

Bowite uses the automatic N to G conversion to to align against all positions in the reference.

RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/

NAME: rsem-prepare-reference
SYNOPSIS: rsem-prepare-reference [options] reference_fasta_file(s) reference_name
DESCRIPTION: The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters. This program is used in conjunction with the 'rsem-calculate-expression' program.
INPUTS: A fasta file of transcripts or A genome sequence fasta file and a GTF gene annotation file. (When using UCSC data, include the related knownIsoforms.txt)