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Forum: Bioinformatics 09-01-2015, 03:00 PM
Replies: 0
Views: 486
Posted By samanta
Scripting for Biology - Online Virtual Classroom-based Module

Hello all,

I am building a number of online virtual classroom-based modules for researchers working on biological data. The description for the first one is attached below, and I will have a beta...
Forum: Bioinformatics 05-20-2015, 05:41 PM
Replies: 0
Views: 997
Posted By samanta
Free Ebook on Bioinformatics Tools - Feel Free to Grab It

Hello all,

I am putting together an ebook to describe a number of useful bioinformatics tools. The book is under development, and V0.1 is freely available at the following link.
...
Forum: Bioinformatics 01-08-2015, 06:45 PM
Replies: 4
Views: 2,001
Posted By samanta
Thanks Genomax. Trimmomatic is part of...

Thanks Genomax.

Trimmomatic is part of Trinity, but I am thinking about moving it in a separate directory. I will look into the rest, but is STAR an unusual aligners after BWA? Do I need to keep...
Forum: Bioinformatics 01-08-2015, 12:13 PM
Replies: 4
Views: 2,001
Posted By samanta
Pandora's Toolbox

Hello,

I am developing a toolbox with collection of source codes of efficient bioinformatics programs.
They are available under the condition that you cite the individual authors and not...
Forum: Oxford Nanopore 09-26-2014, 12:23 PM
Replies: 47
Views: 17,407
Posted By samanta
ten fold compared to what? Check page 13 of...

ten fold compared to what?

Check page 13 of Michael Schatz's slides I posted here.

http://www.homolog.us/blogs/blog/2014/09/26/nanopore-truth-and-nothing-but-the-truth/

Illumina alone - ...
Forum: Oxford Nanopore 09-26-2014, 10:14 AM
Replies: 47
Views: 17,407
Posted By samanta
That is possibly due to the molecule moving...

That is possibly due to the molecule moving through the pore at different speed, and the HMM (Viterbi) calculation for base-calling being fixed at one mode and miscalling in the other mode.

This...
Forum: Oxford Nanopore 09-26-2014, 10:09 AM
Replies: 47
Views: 17,407
Posted By samanta
About a month back, one of my collaborators asked...

About a month back, one of my collaborators asked me to check about Oxford Nanopore, because she was planning to do a large sequencing project with Illumina+Pacbio, and wanted to know whether waiting...
Forum: Bioinformatics 08-21-2014, 08:39 PM
Replies: 5
Views: 1,835
Posted By samanta
The first rule of using Minia assembler: You do...

The first rule of using Minia assembler: You do not talk about Minia assembler.

The second rule of using Minia assembler: You do not talk about Minia assembler.

Third rule of using Minia...
Forum: General 04-11-2014, 04:30 PM
Replies: 17
Views: 5,317
Posted By samanta
A large part of the work is in removing 'tips'...

A large part of the work is in removing 'tips' and 'bubbles' and then simplifying the graph. That is when you do not see any input/output.
Forum: General 04-11-2014, 03:35 PM
Replies: 17
Views: 5,317
Posted By samanta
In the version I worked on two years back for...

In the version I worked on two years back for trying to assemble a large genome (~600MB size), the paired reads needed to be merged into one file.

FASTA Line 1-2 (read1 left)
FASTA Line 3-4...
Forum: General 04-11-2014, 03:33 PM
Replies: 17
Views: 5,317
Posted By samanta
I used to work on velvet several years back, and...

I used to work on velvet several years back, and discussed the code/parameters in our blog many times in those days.

e.g.
...
Forum: Introductions 03-27-2014, 07:54 AM
Replies: 6
Views: 2,057
Posted By samanta
I wrote something up to answer your question - ...

I wrote something up to answer your question -

http://www.homolog.us/blogs/blog/2014/03/27/a-genome-assembly-question/
Forum: Bioinformatics 11-25-2013, 10:37 AM
Replies: 1
Views: 15,093
Posted By samanta
Our blog has some discussion going on between...

Our blog has some discussion going on between Lior Pachter and Istvan that you may find helpful.

http://www.homolog.us/blogs/blog/2013/11/22/cshl-keynote-talk-lior-pachter/
Forum: General 10-14-2013, 10:56 AM
Replies: 6
Views: 3,306
Posted By samanta
some thoughts - ...

some thoughts -

http://www.homolog.us/blogs/blog/2013/10/14/us-science-funding-let-us/
Forum: General 10-14-2013, 10:55 AM
Replies: 6
Views: 5,117
Posted By samanta
Thanks folks. Flxlex, I presume that 730 Mb...

Thanks folks.

Flxlex, I presume that 730 Mb is one time observation, right?
Forum: General 10-05-2013, 10:34 PM
Replies: 6
Views: 3,306
Posted By samanta
You are asking that question in 2013? That is...

You are asking that question in 2013? That is five f***ing years too late.

Look, US financial system went insolvent in 2008. The proper solution would have been to send the bankster crooks to...
Forum: General 10-05-2013, 08:05 AM
Replies: 6
Views: 5,117
Posted By samanta
Pacbio - What is the Typical Throughput?

Based on sparsity of pacbio-related posts, I presume nobody uses the technology. I was at their recent user group meeting and liked the smell of the coffee :)
...
Forum: General 10-05-2013, 07:48 AM
Replies: 6
Views: 3,306
Posted By samanta
It is helping us incredibly. Edit. Not being...

It is helping us incredibly.

Edit. Not being sarcastic.
Forum: Bioinformatics 08-25-2013, 07:32 AM
Replies: 6
Views: 3,980
Posted By samanta
My first guess (based on seeing your...

My first guess (based on seeing your histograms-k29 chart):

Your coverage is very high and that is making the assembler believe that some noisy k-mers are real. One way to check whether that is...
Forum: Bioinformatics 07-30-2013, 07:26 PM
Replies: 4
Views: 1,502
Posted By samanta
Oh well. Please send me an email and I will...

Oh well.

Please send me an email and I will try to walk you through the steps. Maybe we need to start in a different way.
Forum: Bioinformatics 07-29-2013, 10:32 PM
Replies: 4
Views: 1,502
Posted By samanta
Hello, Seems like an interesting problem....

Hello,

Seems like an interesting problem. Here is what you need to do.

(i) Please draw a k-mer distribution of the Illumina reads. I think your Illumina coverage (30) is slightly on the lower...
Forum: General 06-26-2013, 05:08 PM
Replies: 1
Views: 1,525
Posted By samanta
PacBio tutorials

I am developing a set of simple tutorials on PacBio-related algorithms. Please feel free to give your critical input.

http://www.homolog.us/Tutorials/index.php?p=1.1&s=5

Main blog post is here...
Forum: Bioinformatics 05-21-2013, 08:34 PM
Replies: 8
Views: 9,847
Posted By samanta
Here are the links. ...

Here are the links.

http://www.homolog.us/blogs/blog/2013/05/07/genome-assembly-programs-what-hash-functions-do-they-use/
...
Forum: Bioinformatics 05-20-2013, 11:17 AM
Replies: 8
Views: 9,847
Posted By samanta
I would say GPU is a no-go for genome assembly....

I would say GPU is a no-go for genome assembly. We looked at various options for doing genome assembly in GPUs last year, and could not make the algorithms scale well. Genome assembly programs need...
Forum: Bioinformatics 04-10-2013, 05:51 PM
Replies: 18
Views: 29,924
Posted By samanta
Lizhenyu from BGI explained where I made the...

Lizhenyu from BGI explained where I made the error in thinking. When a read has 100 nucleotides and is split into 21-mers, the read will produce only 80 k-mers, not 100. Here is his full response,...
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