From affb1c1de1cd4af947f80f1b6269d781535c4d97 Mon Sep 17 00:00:00 2001 From: langmead Date: Tue, 7 Sep 2010 20:54:17 +0000 Subject: [PATCH] *** empty log message *** --- MANUAL | 18 ++++++++++++++++-- doc/manual.html | 19 ------------------- indexes/e_coli.rev.1.ebwt | Bin 1476941 -> 1476941 bytes 3 files changed, 16 insertions(+), 21 deletions(-) diff --git a/MANUAL b/MANUAL index 4d37aed..9a56cc8 100644 --- a/MANUAL +++ b/MANUAL @@ -19,8 +19,9 @@ Linux, and Solaris. [Bowtie] also forms the basis for other tools, including [TopHat]: a fast splice junction mapper for RNA-seq reads, [Cufflinks]: a tool for transcriptome assembly and isoform quantitiation from RNA-seq reads, -and [Crossbow]: a cloud-computing software tool for large-scale -reseuqncing data. +[Crossbow]: a cloud-computing software tool for large-scale +resequencing data,and [Myrna]: a cloud computing tool for calculating +differential gene expression in large RNA-seq datasets. If you use [Bowtie] for your published research, please cite the [Bowtie paper]. @@ -32,6 +33,7 @@ If you use [Bowtie] for your published research, please cite the [TopHat]: http://tophat.cbcb.umd.edu/ [Cufflinks]: http://cufflinks.cbcb.umd.edu/ [Crossbow]: http://bowtie-bio.sf.net/crossbow +[Myrna]: http://bowtie-bio.sf.net/myrna [Bowtie paper]: http://genomebiology.com/2009/10/3/R25 What isn't Bowtie? @@ -1643,6 +1645,18 @@ format: Fields are separated by tabs. + -e/--ebwt-ref + +By default, when `bowtie-inspect` is run without `-s` or `-n`, it +recreates the reference nucleotide sequences using the bit-encoded +reference nucleotides kept in the `.3.ebwt` and `.4.ebwt` index files. +When `-e/--ebwt-ref` is specified, `bowtie-inspect` recreates the +reference sequences from the Burrows-Wheeler-transformed reference +sequence in the `.1.ebwt` file instead. The reference recreation +process is much slower when `-e/--ebwt-ref` is specified. Also, when +`-e/--ebwt-ref` is specified and the index is in colorspace, the +reference is printed in colors (A=blue, C=green, G=orange, T=red). + -v/--verbose Print verbose output (for debugging). diff --git a/doc/manual.html b/doc/manual.html index 1f80f1b..eb608c3 100644 --- a/doc/manual.html +++ b/doc/manual.html @@ -4119,25 +4119,6 @@ >Use <int> as the seed for pseudo-random number generator.

-
--old-reverse
-
-

bowtie-build versions prior to 0.12.6 would construct the reverse index (in the .rev.1.ebwt and .rev.2.ebwt) by first reversing each unambiguous stretch of nucleotides then concatenating the reversed strings. Starting with bowtie-build 0.12.6, the reverse index is constructed by first concatenating the unambiguous stretches of nucleotides, then reversing the concatenated string. Specify --old-reverse to revert to the old behavior. Both types of index are fully forward and backward compatible, unless otherwise noted.

7