[odysseus]

Thanks for your useful post.

I’m interested in ABySS and I installed it on my linux server.
However, I knew it does not use a reference genome, as it is a de novo assembler.
I think it should be moved from "Align/Assemble to a reference" category to "De novo Align/Assemble" category.

Cheers! ^^

[sci_guy]

...I think it should be moved from "Align/Assemble to a reference" category to "De novo Align/Assemble" category.

Done. Thanks

[Jose Blanca]

Great list!
I'd like to introduce some code I'm working on. I don't know if it deserves to go into the list, but it might be of some use for someone. Is not finished yet, but if someone is interested in trying it out or in working on it just let me know.
You can find it at biolib.
It's a library and a set of script targeted to NGS. There are modules to:
- clean sequences (sanger, 454, ilumina).
- parse caf, ace and bowtie map files.
- clean and filter contigs.
- look for snps and indels.
- filter snps.
- do statistics for: reads, contigs and snps.

Be aware that it's just a work in progress and its in constant flux. The code is available under the AGPL.

[dan]

Beta version of the SEQwiki software database up and running...

Check it out...

http://seqanswers.com/wiki/SEQanswers

http://seqanswers.com/wiki/Software

Dan.

[apfejes]

Hey, that's awesome - Great Job!

[Dinny]

Hi all,

Thanks for the helpful list. Based on reading the post I've tried out Bowtie to align reads from a ChIP-seq experiment run on Illumina GA-II (the facility gave me non-aligned fastq). Worked great!

I want to put the output into cisGenome or FindPeaks (or both). Can anyone advise me how to get it into the right format? Does FindPeaks convert any of the output options in Bowtie?

Thanks

[apfejes]

Hi Dinny,

Findpeaks can use bowtie's reads - but it depends if you want to use PET or SET tags. if you're using PET, you'll need to convert your reads into BED format, which is the only way that you can retain the pairing information. If you're using SET, you should be able to bet Bowtie to produce a .map file (if I recall correctly), which can then be processed natively by FindPeaks.

If you need help with findPeaks, you can always send an email to the mailing list - I tend to reply more quickly to those inquiries than those on SeqAnswers.

Cheers,
Anthony

[ewilbanks]

I don't think that CisGenome has support for bowtie output yet. Best bet would be to find scripts to convert to .bed or .aln

[Dinny]

Thanks very much Anthony and ewilbanks.
I looked closer at Bowtie conversion tools and I can create a .map file from the alignment (I'm working with single-end reads), but I have to get Maq working to do it. I'll give it a go, and compare Maq alignment times while I'm at it ;-)
Cheers,
Dinny

[apfejes]

Hi Dinny,

I think there is also a way to get Bowtie to produce it's own alignment in .map format, if I recall correctly.

Anyhow, if you're working with SET, you can also convert the bowtie reads directly to .bed: https://sourceforge.net/apps/mediawi...e=ConvertToBed

[jsun529]

what is the definition of the header line in SOLiD csfasta file, eg
1_88_1830_R3 -- What is 88, 1830 stands for ? Thanks

[nilshomer]

what is the definition of the header line in SOLiD csfasta file, eg
1_88_1830_R3 -- What is 88, 1830 stands for ? Thanks

See http://seqanswers.com/forums/showthread.php?p=7572.

[Dinny]

Hi Anthony,
Thanks again for the advice. Taking the reads directly into .bed would be better. The .map converter in Bowtie needs a library file created in Maq, so it would be easier to limit the number of applications the data goes through...less opportunity to completely jumble it.
Couldn't see a way to align straight to .map, but I'll look again.
Dinny

[Ka123$]

Solexa findpeaks

Using Findpeaks sort reads on bowtie mapped alignment is taking up too much memory......!!!!! So I am trying using the GERALD maps reads directly from solexa to convert to wig files...I believe the solexa GERALD mapped alignments are ELAND format?
So the aligner type will be -aligner eland, to perform separateReads.jar?
Any suggestions?

[apfejes]

Hi Ka123,

There are other ways to do the sort - including several methods you could try from the linux command line. However, I'm really not sure why it's taking so memory. Could you give me a few ideas as to what your work flow is?

In the meantime, documentation and an example command for SeparateReads can be found here:

https://sourceforge.net/apps/mediawiki/vancouvershortr/index.php?title=SeparateReads