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Old 06-01-2010, 07:13 PM   #1
john_mu
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Lightbulb SpliceMap 3.2.1: Announcing addition of Bowtie support

Hi SEQanswers community,

Bowtie support has just been added to SpliceMap.

Please check the website to download the new version.

http://www-stat.stanford.edu/~kinfai...Map/index.html

With Bowtie support comes some requested features
  • Support for FASTQ and FASTA file formats
  • Mac OS X support
  • Less memory usage when sorting SAM file
  • Faster

Let me know what you think of the new input format. I felt that is was much clearer an easier to customize. However, your feedback is important to me.

Please let me know if you find any part hard to use or unintuitive. I will see what I can do.

Also, after further testing, the "Try Harder" option in Bowtie didn't seem to make much difference... Currently, it is default to on. However, if you want to save 10-15% of your running time, it is probably ok to turn it off.

Next, I will add read quality to the SAM output and hopefully (if there are no more major usability issues) have some time to work on algorithmic improvements.
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Old 06-01-2010, 09:31 PM   #2
thinkRNA
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how does SpliceMap perform when aligning via bowtie versus its default aligner (seqMap)? Can you point out any pros/cons?

how can I run spliceMap using the "-best" option and did you test bowtie's different parameters such that you can recommend which ones are most compatible for ideal splice isoform assembly using SpliceMap?

Thanks so much for your efforts!
Priyam
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Old 06-01-2010, 09:42 PM   #3
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Hi Priyam,

The output is basically the same as SeqMap and Eland according to the sequence data that I have (about 100 junctions different out of 170k).

Pros: Faster, uses less memory(compared to SeqMap, but not Eland), multi-threaded, free (compared to Eland, not SeqMap).
Cons: Need to obtain separate bowtie-index, not developed by our lab (so less control).

The -best option is set by default and cannot be changed, since that is required by SpliceMap. You don't need to worry about the settings on Bowtie. It is called by SpliceMap automatically and the settings used are the best ones we determined from testing. "try harder" is given as an option since the effect of that is undetermined.


John Mu
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Old 06-02-2010, 05:09 PM   #4
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Just an update, some people are having trouble building this from source on the latest version of GCC/G++ due to some stricter requirements on libraries.

Once my exams are over we'll release an update for that.

Also, it seems the sensitivity is not as good as what we would like for 125bp reads. We'll have an update for this soon too. However, the specificity is consistently very good.

Does anyone know any links to publicly available 125bp+ RNA-seq reads (from a mammalian genome)? This will save me some time in searching the databases
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Old 06-03-2010, 07:28 AM   #5
xguo
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Quote:
Originally Posted by john_mu View Post
Hi SEQanswers community,

Bowtie support has just been added to SpliceMap.

Please check the website to download the new version.

http://www-stat.stanford.edu/~kinfai...Map/index.html

With Bowtie support comes some requested features
  • Support for FASTQ and FASTA file formats
  • Mac OS X support
  • Less memory usage when sorting SAM file
  • Faster

Let me know what you think of the new input format. I felt that is was much clearer an easier to customize. However, your feedback is important to me.

Please let me know if you find any part hard to use or unintuitive. I will see what I can do.

Also, after further testing, the "Try Harder" option in Bowtie didn't seem to make much difference... Currently, it is default to on. However, if you want to save 10-15% of your running time, it is probably ok to turn it off.

Next, I will add read quality to the SAM output and hopefully (if there are no more major usability issues) have some time to work on algorithmic improvements.
Great new!! Have you tested it on SOLiD color space reads?

thanks
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Old 06-03-2010, 08:44 AM   #6
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Quote:
Originally Posted by xguo View Post
Great new!! Have you tested it on SOLiD color space reads?

thanks
Sorry xguo, that's not yet supported. We will look into that over summer. Currently there is no hard timeline for color-space support, we have a few more things that need to be done first.

I know bowtie can align colour-space reads, but this also needs to be supported by the junction search, which needs some thought.

Sorry about that!
John Mu
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Old 06-05-2010, 07:44 PM   #7
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Just an update, I modified the sources and instructions to help people build it from source. We have been getting some people reporting that it won't compile on certain versions of g++.
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