Mercurial > repos > bjoern-gruening > bismark

annotate bismark_wrapper/README @ 1:183de9d00131 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
add indices.loc files
author bjoern-gruening
date Tue, 25 Dec 2012 05:52:28 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
1
183de9d00131 add indices.loc files
bjoern-gruening
parents:
diff changeset
1 Bismark uses Bowtie or Bowtie2 to map the reads.
183de9d00131 add indices.loc files
bjoern-gruening
parents:
diff changeset
2 Create your reference index with bismark_genome_preparation in your
183de9d00131 add indices.loc files
bjoern-gruening
parents:
diff changeset
3 normal Bowtie2/Botwie index directory.
183de9d00131 add indices.loc files
bjoern-gruening
parents:
diff changeset
4 bismark_genome_preparation will create a Bisulfite_Genome folder directly in
183de9d00131 add indices.loc files
bjoern-gruening
parents:
diff changeset
5 your Bowtie2/Bowtie index directory. If you follow that approach you do not
183de9d00131 add indices.loc files
bjoern-gruening
parents:
diff changeset
6 need to specify or modify an extra *.loc file.
183de9d00131 add indices.loc files
bjoern-gruening
parents:
diff changeset
7 That wrapper will extract the path to the Bisulfite_Genome folder from
183de9d00131 add indices.loc files
bjoern-gruening
parents:
diff changeset
8 ./tool-data/bowtie2_indices.loc or ./tool-data/bowtie_indices.loc.