[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.

[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

[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

[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

[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

[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

[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]

Hey, that's awesome - Great Job!

[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.

[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.

[sci_guy]

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

Done. Thanks

[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]

Further to the above, if you're a molecular biologist without coding skills it is far easier to stick to commercial integrated solutions however you may feel constrained by lack of features within the software if your application is anything other than vanilla.
If you embark upon the open source route you'll need skills in UNIX shell scripting/Perl/SQL. If you don't have them get a bioinformatician onboard. If you need to do 'counting' methods such as RNA-Seq, CHiP-Seq, Bis-Seq, etc then it is probably wise to consult a biostatistician.

[apfejes]

Hi hrajasim,

That's a very open ended question, depending very strongly on what type of analysis you'd like to do. As far as I'm aware, the cutting edge development for NGS is happening in open source, so you'll probably want to fill major parts of the pipeline with open source (Eg, aligners, format converters, ChIP-Seq analysis, assembly, etc)

However, any time you're contrasting open source versus a commercial product, you have to ask the right questions:

Is there a feature set that I absolutely need?

Will I require support for the software beyond the forums and available community?

Will I want to make modifications to the source code and customize it for the pipeline?

Without knowing what you plan to do with the software, it will be impossible for us to figure out which path is best for you.

Cheers!

[hrajasim]

Open source Vs Commercial

Hi Folks, I an new to NGS and am tasked to evaluate commercial and open source alternatives to analyse NGS data. Looking at the pretty comprehensive list in this post (which is very useful) I am not able to make out whether we really need to pay for a solution such as Genomatix or can we do away with just the free open source tools?

Please comment or share your thoughts in this regard.

I Appreciate your time and inputs.
Thanks,