SeqSaw 
Short Spliced Sequence Mapping Tool
A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.
SeqSaw
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> |
| 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.
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
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 |
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.
Comments, suggestions, questions, bug reports, etc, are all welcome. For enquiries, please send email to wanglikun at tsinghua.edu.cn.
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.
