- Added poly(A) tails to 'reference_name.transcripts.fa' so that the RSEM generated...

[rsem.git] / README.md

diff --git a/README.md b/README.md
index 1e64574d8683f73779cad2bc95a32eb9001c1d52..4b0b3ec6bbea187f13a41dfeb8fb873aaa3b1d36 100644 (file)
--- a/README.md
+++ b/README.md
@@ -147,7 +147,27 @@ unsorted BAM file, 'sample_name.genome.sorted.bam' and
 generated by the samtools included. All these files are in genomic
 coordinates.
 
-#### a) Generating a Wiggle file
+#### a) Converting transcript BAM file into genome BAM file
+
+Normally, RSEM will do this for you via '--output-genome-bam' option
+of 'rsem-calculate-expression'. However, if you have run
+'rsem-prepare-reference' and use 'reference_name.idx.fa' to build
+indices for your aligner, you can use 'rsem-tbam2gbam' to convert your
+transcript coordinate BAM alignments file into a genomic coordinate
+BAM alignments file without the need to run the whole RSEM
+pipeline. Please note that 'rsem-prepare-reference' will convert all
+'N' into 'G' by default for 'reference_name.idx.fa'. If you do not
+want this to happen, please use '--no-ntog' option.
+
+Usage:
+
+    rsem-tbam2gbam reference_name unsorted_transcript_bam_input genome_bam_output
+
+reference_name                   : The name of reference built by 'rsem-prepare-reference'                             
+unsorted_transcript_bam_input    : This file should satisfy: 1) the alignments of a same read are grouped together, 2) for any paired-end alignment, the two mates should be adjacent to each other, 3) this file should not be sorted by samtools 
+genome_bam_output                : The output genomic coordinate BAM file's name
+
+#### b) Generating a Wiggle file
 
 A wiggle plot representing the expected number of reads overlapping
 each position in the genome/transcript set can be generated from the
@@ -162,9 +182,9 @@ Usage:
 sorted_bam_input        : Input BAM format file, must be sorted  
 wig_output              : Output wiggle file's name, e.g. output.wig  
 wiggle_name             : the name of this wiggle plot  
---no-fractional-weight  : If this is set, RSEM will not look for "ZW" tag and each alignment appeared in the BAM file has weight 1. Set this if your BAM file is not generated by RSEM. Please note that this option must be at the end of the command line.
+--no-fractional-weight  : If this is set, RSEM will not look for "ZW" tag and each alignment appeared in the BAM file has weight 1. Set this if your BAM file is not generated by RSEM. Please note that this option must be at the end of the command line
 
-#### b) Loading a BAM and/or Wiggle file into the UCSC Genome Browser or Integrative Genomics Viewer(IGV)
+#### c) Loading a BAM and/or Wiggle file into the UCSC Genome Browser or Integrative Genomics Viewer(IGV)
 
 For UCSC genome browser, please refer to the [UCSC custom track help page](http://genome.ucsc.edu/goldenPath/help/customTrack.html).
 
@@ -174,7 +194,7 @@ Here are some guidance for visualizing transcript coordinate files using IGV:
 
 1) Import the transcript sequences as a genome 
 
-Select File -> Import Genome, then fill in ID, Name and Fasta file. Fasta file should be 'reference_name.idx.fa'. After that, click Save button. Suppose ID is filled as 'reference_name', a file called 'reference_name.genome' will be generated. Next time, we can use: File -> Load Genome, then select 'reference_name.genome'.
+Select File -> Import Genome, then fill in ID, Name and Fasta file. Fasta file should be 'reference_name.transcripts.fa'. After that, click Save button. Suppose ID is filled as 'reference_name', a file called 'reference_name.genome' will be generated. Next time, we can use: File -> Load Genome, then select 'reference_name.genome'.
 
 2) Load visualization files
 
@@ -182,7 +202,7 @@ Select File -> Load from File, then choose one transcript coordinate visualizati
 
     igvtools tile reference_name.transcript.wig reference_name.transcript.tdf reference_name.genome   
  
-#### c) Generating Transcript Wiggle Plots
+#### d) Generating Transcript Wiggle Plots
 
 To generate transcript wiggle plots, you should run the
 'rsem-plot-transcript-wiggles' program.  Run 
@@ -192,7 +212,7 @@ To generate transcript wiggle plots, you should run the
 to get usage information or visit the [rsem-plot-transcript-wiggles
 documentation page](http://deweylab.biostat.wisc.edu/rsem/rsem-plot-transcript-wiggles.html).
 
-#### d) Visualize the model learned by RSEM
+#### e) Visualize the model learned by RSEM
 
 RSEM provides an R script, 'rsem-plot-model', for visulazing the model learned.