From ac8b7376ccc650536aaa353df7c0b8ee50fc39ab Mon Sep 17 00:00:00 2001 From: Bo Li Date: Thu, 17 Feb 2011 09:12:25 -0600 Subject: [PATCH] v1.1.2 --- README.txt | 6 +----- rsem-calculate-expression | 4 ++-- 2 files changed, 3 insertions(+), 7 deletions(-) diff --git a/README.txt b/README.txt index 3ef2603..0a76a6f 100644 --- a/README.txt +++ b/README.txt @@ -66,7 +66,7 @@ documentation page](rsem-prepare-reference.html). ### II. Calculating Expression Values -To prepare the reference sequences, you should run the +To calculate expression values, you should run the 'rsem-calculate-expression' program. Run rsem-calculate-expression --help @@ -74,10 +74,6 @@ To prepare the reference sequences, you should run the to get usage information or visit the [rsem-calculate-expression documentation page](rsem-calculate-expression.html). -Note: RSEM no longer provides nu values. Instead, RSEM provides -nrf(normalized read fraction), which is a normalized version of theta -vector excluding theta_0. - #### Calculating expression values from single-end data For single-end models, users have the option of providing a fragment diff --git a/rsem-calculate-expression b/rsem-calculate-expression index 3539fa4..de412ae 100755 --- a/rsem-calculate-expression +++ b/rsem-calculate-expression @@ -396,7 +396,7 @@ Comma-separated list of files containing downstream reads which are paired with =item B -SAM/BAM formatted input file. If "-" is specified for the filename, SAM/BAM input is instead assumed to come from standard input. SAM/BAM format used is SAM Spec v1.2. RSEM requires all alignments of the same read group together. For paired-end reads, RSEM also requires the two mates of any alignment be adjacent. See Description section for how to make input file obey RSEM's requirements. +SAM/BAM formatted input file. If "-" is specified for the filename, SAM/BAM input is instead assumed to come from standard input. RSEM requires all alignments of the same read group together. For paired-end reads, RSEM also requires the two mates of any alignment be adjacent. See Description section for how to make input file obey RSEM's requirements. =item B @@ -538,7 +538,7 @@ One simple way to make the alignment file (e.g. input.sam) satisfying RSEM's req sort -k 1,1 -s input.sam > input.sorted.sam -The SAM/BAM format RSEM uses is v1.2. +The SAM/BAM format RSEM uses is v1.3. However, it is compatible with old SAM/BAM format. The user must run 'rsem-prepare-reference' with the appropriate reference before using this program. -- 2.39.2