Revision history for QRidgeWalker


Revision [7404]

Last edited on 2015-01-18 18:02:36 by XianwenRen
Additions:
[[https://sites.google.com/site/renxwise/home/qridge QRidge]]
Deletions:
[[http://zhangroup.aporc.org/images/files/QridgeAssemblerFast.zip QRidge]]

Revision [7403]

Edited on 2015-01-18 18:01:18 by XianwenRen
Additions:
Xianwen Ren and Qi Jin. Restoring transcriptomes from shotgun RNA-Seq data through quantitative sequence transformation. Submitted.
Deletions:
Xianwen Ren and Qi Jin. Restoring authentic transcriptomes from shotgun RNA-Seq data through sequence transformation. Submitted.

Revision [7187]

Edited on 2014-09-20 06:40:33 by XianwenRen

No Differences

Revision [7186]

Edited on 2014-09-20 06:40:02 by XianwenRen
Additions:
%%QRidge.pl <Fasta> <KmerSize> <MinCoverage> <MinContigLength> <Mode:Comprehensive|Concise>%%
Here,
<Fasta>: Specify the path to the reads file, requiring the fasta format; For paired-end sequencing, the two reads files should be concatenated to one single fasta file.
<KmerSize>: Specify the size of kmers. The values can be any number smaller than the read length, generally 25.
<MinCoverage>: Specify the minimum allowed frequency for each kmer. Kmers with frequency smaller than MinCoverage will be deleted. MinCoverage=1 is the most sensitive.
<MinContigLength>: Only contigs longer than MinContigLength will be printed.
<Mode:Comprehensive|Concise>: The program provides two assembly modes. One is specified by 0, i.e., the comprehensive mode; the other is specified by 1, i.e., the concise mode. Comprehensive mode allows repeated kmers within and between contigs; concise mode only allows repeated kmers within contigs but does not allow repeated kmers between contigs. Comprehensive mode is more sensitive but slower.
An example:
%%QRidge.pl reads.fasta 25 1 100 0 >contigs.fasta%%
Deletions:
QRidge.pl <Fasta> <KmerSize> <MinCoverage> <MinContigLength> <Mode:Comprehensive|Concise>
**<Fasta>**: Specify the path to the reads file, requiring the fasta format; For paired-end sequencing, the two reads files should be concatenated to one single fasta file.
**<KmerSize>**: Specify the size of kmers. The values can be any number smaller than the read length, generally 25.
**<MinCoverage>**: Specify the minimum allowed frequency for each kmer. Kmers with frequency smaller than MinCoverage will be deleted. MinCoverage=1 is the most sensitive.
**<MinContigLength>**: Only contigs longer than MinContigLength will be printed.
**<Mode:Comprehensive|Concise>**: The program provides two assembly modes. One is specified by 0, i.e., the comprehensive mode; the other is specified by 1, i.e., the concise mode. Comprehensive mode allows repeated kmers within and between contigs; concise mode only allows repeated kmers within contigs but does not allow repeated kmers between contigs. Comprehensive mode is more sensitive but slower.
An example: QRidge.pl reads.fasta 25 1 100 0 >contigs.fasta

Revision [7185]

Edited on 2014-09-20 06:37:28 by XianwenRen
Additions:
**<Fasta>**: Specify the path to the reads file, requiring the fasta format; For paired-end sequencing, the two reads files should be concatenated to one single fasta file.
**<KmerSize>**: Specify the size of kmers. The values can be any number smaller than the read length, generally 25.
**<MinCoverage>**: Specify the minimum allowed frequency for each kmer. Kmers with frequency smaller than MinCoverage will be deleted. MinCoverage=1 is the most sensitive.
**<MinContigLength>**: Only contigs longer than MinContigLength will be printed.
**<Mode:Comprehensive|Concise>**: The program provides two assembly modes. One is specified by 0, i.e., the comprehensive mode; the other is specified by 1, i.e., the concise mode. Comprehensive mode allows repeated kmers within and between contigs; concise mode only allows repeated kmers within contigs but does not allow repeated kmers between contigs. Comprehensive mode is more sensitive but slower.
Deletions:
**<Fasta>**: Specify the path to the reads file, requiring the fasta format; For paired-end sequencing, the two reads files should be concatenated to one single fasta file.
**<KmerSize>**: Specify the size of kmers. The values can be any number smaller than the read length, generally 25.
**<MinCoverage>**: Specify the minimum allowed frequency for each kmer. Kmers with frequency smaller than MinCoverage will be deleted. MinCoverage=1 is the most sensitive.
**<MinContigLength>**: Only contigs longer than MinContigLength will be printed.
**<Mode:Comprehensive|Concise>**: The program provides two assembly modes. One is specified by 0, i.e., the comprehensive mode; the other is specified by 1, i.e., the concise mode. Comprehensive mode allows repeated kmers within and between contigs; concise mode only allows repeated kmers within contigs but does not allow repeated kmers between contigs. Comprehensive mode is more sensitive but slower.

Revision [7184]

Edited on 2014-09-20 06:31:44 by XianwenRen
Additions:
An example: QRidge.pl reads.fasta 25 1 100 0 >contigs.fasta
Deletions:
Example: QRidge.pl reads.fasta 25 1 100 0 >contigs.fasta

Revision [7183]

Edited on 2014-09-20 06:31:06 by XianwenRen
Additions:
=====Usage:=====
QRidge.pl <Fasta> <KmerSize> <MinCoverage> <MinContigLength> <Mode:Comprehensive|Concise>
**<Fasta>**: Specify the path to the reads file, requiring the fasta format; For paired-end sequencing, the two reads files should be concatenated to one single fasta file.
**<KmerSize>**: Specify the size of kmers. The values can be any number smaller than the read length, generally 25.
**<MinCoverage>**: Specify the minimum allowed frequency for each kmer. Kmers with frequency smaller than MinCoverage will be deleted. MinCoverage=1 is the most sensitive.
**<MinContigLength>**: Only contigs longer than MinContigLength will be printed.
**<Mode:Comprehensive|Concise>**: The program provides two assembly modes. One is specified by 0, i.e., the comprehensive mode; the other is specified by 1, i.e., the concise mode. Comprehensive mode allows repeated kmers within and between contigs; concise mode only allows repeated kmers within contigs but does not allow repeated kmers between contigs. Comprehensive mode is more sensitive but slower.
Example: QRidge.pl reads.fasta 25 1 100 0 >contigs.fasta

Revision [7182]

Edited on 2014-09-19 10:12:20 by XianwenRen
Additions:
[[http://zhangroup.aporc.org/images/files/QridgeAssemblerFast.zip QRidge]]
Deletions:
[[http://zhangroup.aporc.org/AttachedFiles/files.xml?action=download&file=QridgeAssemblerFast.zip QRidge]]

Revision [7030]

Edited on 2014-08-09 22:08:28 by XianwenRen
Additions:
=====Function:=====
Deletions:
=====Funciont:=====

Revision [7029]

Edited on 2014-08-09 22:07:57 by XianwenRen
Additions:
=====Author:=====
Deletions:
=====Authors:=====

Revision [7027]

Edited on 2014-08-09 21:35:17 by XianwenRen
Additions:
=====Software:=====
[[http://zhangroup.aporc.org/AttachedFiles/files.xml?action=download&file=QridgeAssemblerFast.zip QRidge]]

=====Authors:=====
Xianwen Ren, [[http://www.ipbcams.ac.cn Institute of Pathogen Biology, CAMS]]

=====Funciont:=====
Given a set of RNA-Seq data, QRidge assembles the short reads into long full-length transcripts.

=====Reference:=====
Xianwen Ren and Qi Jin. Restoring authentic transcriptomes from shotgun RNA-Seq data through sequence transformation. Submitted.
Deletions:
[[http://zhangroup.aporc.org/AttachedFiles/files.xml?action=download&file=QridgeAssemblerFast.zip QRidgeWalker]]

Revision [6755]

The oldest known version of this page was created on 2013-09-22 15:34:15 by XianwenRen
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