@@ -78,7 +78,7 @@ For the pipeline settings, there are some values that you need to specify while
1.`output_dir`: path to output directory (if it does not exist, Gentrap will create it for you).
2.`aligner`: which aligner to use (`gsnap` or `tophat`)
3.`reference`: this must point to a reference FASTA file and in the same directory, there must be a `.dict` file of the FASTA file.
3.`reference_fasta`: this must point to a reference FASTA file and in the same directory, there must be a `.dict` file of the FASTA file.
4.`expression_measures`: this entry determines which expression measurement modes Gentrap will do. You can choose zero or more from the following: `fragments_per_gene`, `bases_per_gene`, `bases_per_exon`, `cufflinks_strict`, `cufflinks_guided`, and/or `cufflinks_blind`. If you only wish to align, you can set the value as an empty list (`[]`).
5.`strand_protocol`: this determines whether your library is prepared with a specific stranded protocol or not. There are two protocols currently supported now: `dutp` for dUTP-based protocols and `non_specific` for non-strand-specific protocols.
6.`annotation_refflat`: contains the path to an annotation refFlat file of the entire genome
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@@ -100,7 +100,7 @@ Thus, an example settings configuration is as follows: