Mercurial > repos > fubar > rgrnastar_203e
changeset 11:94c94e25d61c draft
Uploaded
| author | fubar |
|---|---|
| date | Mon, 12 Aug 2013 05:18:07 -0400 |
| parents | 1ce3d6f45fbc |
| children | f81bf1f1d924 |
| files | rgrnastar/rg_rnaStar.xml |
| diffstat | 1 files changed, 6 insertions(+), 3 deletions(-) [+] |
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--- a/rgrnastar/rg_rnaStar.xml Mon Aug 12 05:07:28 2013 -0400 +++ b/rgrnastar/rg_rnaStar.xml Mon Aug 12 05:18:07 2013 -0400 @@ -245,14 +245,17 @@ strand (i.e. containing only non-canonical junctions) will be suppressed. If you have stranded RNA-seq data, you do not need to use any specific STAR options. Instead, you need -to run Cufflinks with the library option --library-type options. For example, cufflinks <...> - -library-type fr-firststrand should be used for the “standard” dUTP protocol. This option has -to be used only for Cufflinks runs and not for STAR runs. +to run Cufflinks with the library option --library-type options. For example, cufflinks with +library-type fr-firststrand should be used for the “standard” dUTP protocol. +This option has to be used only for Cufflinks runs and not for STAR runs. It is recommended to remove the non-canonical junctions for Cufflinks runs using – + --outFilterIntronMotifs RemoveNoncanonical filter out alignments that contain non-canonical junctions + OR + --outFilterIntronMotifs RemoveNoncanonicalUnannotated filter out alignments that contain non-canonical unannotated junctions when using annotated splice junctions database. The annotated non-