SeqSaw seqSaw

Short Spliced Sequence Mapping Tool

A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.

Authors Likun Wang, Xiaowo Wang, Xi Wang, Yanchun Liang, Xuegong Zhang
Maintainer Likun Wang <wanglikun at tsinghua.edu.cn>

Download

Package source SeqSaw_1.0.8.tar.gz
Package with examples SeqSaw_1.0.8_examples.tar.gz
Animated Slides (PDF) Mini_example.pdf
SeqSaw Method (PDF) Method.pdf (mini example in detail)
Download from SourceForge SeqSaw Project (all files) ~new~

Note: SeqSaw_1.0.8.tar.gz is newly realeased at Aug 10 2011. SourceForge is no longer supporting Internet Explorer 6. If there are problems with the download, please check your browser's security bar, or try another mirror, or contact us.

How to use

Step 1: Map reads to the reference genome allowing long gaps
Step 2: Predict splice junctions upon the mapping results
Step 3: Remap reads only allowing spanning predicted junctions (optional)
Input and output format (with examples)
Reliability factors for optional filtering

System Requirements

The RAM requirement is related to the number of reads. At least 4GB RAM is required. However, 32GB RAM is recommended. As an example, we mapped 30M 75-nt paired-end reads to hg18 to measure the memory used by SeqSaw.

Number of cores used Memory used per core Memory used in total (VIRT)      Total time used            Command      
1 core ~ 22 G ~ 22 G ~ 6 days seqsaw  mapper run.cfg
4 cores ~ 7.2 G ~ 29 G ~ 45 hours runSeqSaw.pl    mapper run.cfg  4
6 cores ~ 5.5 G ~ 33 G ~ 30 hours runSeqSaw.pl    mapper run.cfg  6
4 cores X 2 servers ~ 4.7 G ~ 19 G X 2 servers ~ 23 hours runSeqSaw2.pl  mapper run.cfg  4  2
8 cores X 2 servers ~ 3.5 G ~ 28 G X 2 servers ~ 15 hours runSeqSaw2.pl  mapper run.cfg  8  2

Supplementary data

Junctions predicted by SeqSaw from HUVEC RNA-seq data (hg18)
Junctions predicted by SeqSaw from NHEK RNA-seq data (hg18)
The above junctions are predicted by the old version SeqSaw 1.0.1.

Feedback

Comments, suggestions, questions, bug reports, etc, are all welcome. For enquiries, please send email to wanglikun at tsinghua.edu.cn.

Acknowledgement

This package adopted some data structures from the package SeqMap (Jiang et al. 2008).

Anyone can use the source codes and executable files of SeqSaw free of charge for non-commercial use. Valid XHTML 1.0 Strict Valid CSS!