Hi SEQanswers Community,
SpliceMap has received significant updates, with numerous bugs fixed. If you were having trouble with the old version, please try this new one.
New webpage: http://www-stat.stanford.edu/~kinfai/SpliceMap/
The new webpage has a detailed tutorial/manual to help you along.
In the next point release we will add Bowtie support for the short reads mapping. I realize that not many of you have access to Eland and this is inconvenient as SeqMap is quite slow (but very accurate)...
In the next version you can use the workflow: Bowtie -> SpliceMap -> Cufflinks.
Let me know if you have trouble with using the SAM output with Cufflinks.
The source code is now included so you can compile the code for your
own platform. It should work on any version of Linux.
---
Notable New features:
---
Comparison to Tophat with 23 million (50bp) reads mapped to the human genome (hg18). EST validation was used to judge specificity.
I tested randomly filtering out unreliable junctions until the total number of junctions found is about the same as Tophat and the specificity in that case is about 90%, which is still an improvement over Tophat.
details here: http://www-stat.stanford.edu/~kinfai.../features.html
SpliceMap has received significant updates, with numerous bugs fixed. If you were having trouble with the old version, please try this new one.
New webpage: http://www-stat.stanford.edu/~kinfai/SpliceMap/
The new webpage has a detailed tutorial/manual to help you along.
In the next point release we will add Bowtie support for the short reads mapping. I realize that not many of you have access to Eland and this is inconvenient as SeqMap is quite slow (but very accurate)...
In the next version you can use the workflow: Bowtie -> SpliceMap -> Cufflinks.
Let me know if you have trouble with using the SAM output with Cufflinks.
The source code is now included so you can compile the code for your
own platform. It should work on any version of Linux.
---
Notable New features:
- SAM format support (sorted for use in cufflinks)
- Many bugs fixed (sorry about that )
- More accurate coverage calculation
- Faster junction search
- and more!
---
Comparison to Tophat with 23 million (50bp) reads mapped to the human genome (hg18). EST validation was used to judge specificity.
Code:
SpliceMap (Depending on level of filtering) Junctions found 169,098 121,200 EST validated 143,840 114,661 Novel junctions 31,155 7,521 Specificity (EST) 85.06% 94.60%
Code:
Tophat Junctions found 133,722 EST validated 117,113 Novel junctions 19,777 Specificity (EST) 87.58%
details here: http://www-stat.stanford.edu/~kinfai.../features.html
Comment