Commit 2dfc156d authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.3.1+dfsg

parent 782bbe2e

Gibbs.cpp

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@@ -432,7 +432,7 @@ int main(int argc, char* argv[]) { 
    printf("- One isoform's prior per line\n");

    printf("- Priors must be in the same order as in the .ti file\n");

    printf("- Priors for those to-be-omitted isoforms must be included as well\n");

    printf("- Comments can be added after prior seperated by space(s)\n");

    printf("- Comments can be added after prior separated by space(s)\n");

		exit(-1);

	}

README.md

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@@ -12,6 +12,7 @@ Table of Contents 
* [Compilation & Installation](#compilation)

* [Usage](#usage)

    * [Build RSEM references using RefSeq, Ensembl, or GENCODE annotations](#built)

    * [Build RSEM references for untypical organisms](#untypical)

* [Example](#example-main)

* [Simulation](#simulation)

* [Generate Transcript-to-Gene-Map from Trinity Output](#gen_trinity)
@@ -216,6 +217,20 @@ rsem-prepare-reference --gtf gencode.v24.annotation.gtf \ 
Similar to Ensembl annotation, if you want to use GFF3 files (not

recommended), add option `--gff3-RNA-patterns transcript`.



#### <a name="untypical"></a> Build RSEM references for untypical organisms



For untypical organisms, such as viruses, you may only have a GFF3 file that containing only genes but not any transcripts. You need to turn on `--gff3-genes-as-transcripts` so that RSEM will make each gene as a unique transcript.



Here is an example command:



```

rsem-prepare-reference --gff3 virus.gff \

               --gff3-genes-as-transcripts \

               --bowtie \

               virus.genome.fa \

               ref/virus

```



### II. Calculating Expression Values



To calculate expression values, you should run the

convert-sam-for-rsem

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@@ -56,11 +56,7 @@ __END__ 


=head1 NAME



convert-sam-for-rsem



=head1 PURPOSE



Make a RSEM compatible BAM file.

convert-sam-for-rsem - Make a RSEM compatible BAM file.



=head1 SYNOPSIS

pRSEM/File.py

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@@ -10,7 +10,7 @@ class File: 
    self.fullname = None  ## file's full name, include dir, base, and all ext

    self.is_gz    = None  ## if file is gzipped

    self.dirname  = None  ## directory name

    self.basename = None  ## base name sans all extension seperated by dot

    self.basename = None  ## base name sans all extension separated by dot

    self.filename_sans_ext = None ## no path, no last extension sep by dot

rsem-calculate-expression

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@@ -774,11 +774,7 @@ __END__ 


=head1 NAME



rsem-calculate-expression



=head1 PURPOSE



Estimate gene and isoform expression from RNA-Seq data.

rsem-calculate-expression - Estimate gene and isoform expression from RNA-Seq data.



=head1 SYNOPSIS
@@ -1125,7 +1121,7 @@ Using a logistic regression to combine TSS signals from multiple complementary d 


=back



Parameters for all the above models are learned from a training set. For detailed explainations, please see prior-enhanced RSEM's paper. (Default: 'pk')

Parameters for all the above models are learned from a training set. For detailed explanations, please see prior-enhanced RSEM's paper. (Default: 'pk')



=back