Mercurial > repos > bgruening > bismark

annotate README @ 13:7a143c7b3f1b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author bgruening
date Tue, 13 Nov 2012 13:32:56 -0500
parents 221e740377ca
children 73508c5b4273
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
221e740377ca Uploaded
bgruening
parents:
diff changeset
1 Bismark uses Bowtie or Bowtie2 to map the reads.
221e740377ca Uploaded
bgruening
parents:
diff changeset
2 Create your reference index with bismark_genome_preparation in your
221e740377ca Uploaded
bgruening
parents:
diff changeset
3 normal Bowtie2/Botwie index directory.
221e740377ca Uploaded
bgruening
parents:
diff changeset
4 bismark_genome_preparation will create a Bisulfite_Genome folder directly in
221e740377ca Uploaded
bgruening
parents:
diff changeset
5 your Bowtie2/Bowtie index directory. If you follow that approach you do not
221e740377ca Uploaded
bgruening
parents:
diff changeset
6 need to specify or modify an extra *.loc file.
221e740377ca Uploaded
bgruening
parents:
diff changeset
7 That wrapper will extract the path to the Bisulfite_Genome folder from
221e740377ca Uploaded
bgruening
parents:
diff changeset
8 ./tool-data/bowtie2_indices.loc or ./tool-data/bowtie_indices.loc.