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Search: Posts Made By: gprakhar
Forum: Bioinformatics 08-05-2014, 12:13 AM
Replies: 13
Views: 4,487
Posted By gprakhar
Hello, I do understand that the...

Hello,

I do understand that the pre-processing for MiSeq Paired End data is different.
For my data I first assemble the Paired end reads, using PANDAseq. So no need for split_libraries.py

As...
Forum: Bioinformatics 08-04-2014, 11:53 PM
Replies: 13
Views: 4,487
Posted By gprakhar
The sequencing was done by a third party...

The sequencing was done by a third party sequencing provider (http://www.scigenom.com/).
On requesting them for (1) Adapter sequences, (2) barcode and (3) Primer sequence for assembling the Paired...
Forum: Bioinformatics 08-04-2014, 11:46 PM
Replies: 13
Views: 4,487
Posted By gprakhar
I am still not clear about what exactly should I...

I am still not clear about what exactly should I use as SampleId in the Qiime mapping file.
But from this post I assume a part of fastq header can be used for this to identify the samples uniquely,...
Forum: Bioinformatics 08-04-2014, 11:42 PM
Replies: 13
Views: 4,487
Posted By gprakhar
So that means that in the Qiime mapping file I...

So that means that in the Qiime mapping file I can use any barcode sequence, it only has be a unique one for each sample & same for all replicates of a sample ?

According to my understanding of...
Forum: Bioinformatics 08-04-2014, 02:43 AM
Replies: 13
Views: 4,487
Posted By gprakhar
bump. For a MiSeq V3 Data set multiple...

bump.

For a MiSeq V3 Data set multiple samples (3 replicate per sample), with barcode used but sequence not available, how to create a meta-data file so the samples can be associated by Qiime with...
Forum: Bioinformatics 07-31-2014, 02:59 AM
Replies: 13
Views: 4,487
Posted By gprakhar
Question Regarding Qiime Metadata Mapping File

Hello,

Library specs: Paired End, Read length 150 bp, V3 region 16S rRNA gene
Platform : MiSeq, Illumina
Experiment : Wheat Field, rhizosphere samples, Elevated CO2 and temperature...
Forum: Bioinformatics 03-24-2014, 11:28 PM
Replies: 1
Views: 816
Posted By gprakhar
The hmmer tool, is your best bet for searching a...

The hmmer tool, is your best bet for searching a nucleotide sequence with a hmm model.
For a detailed appreciation of hmm model use and lot of examples please refer to the
hmmer 3 documentation...
Forum: Bioinformatics 03-21-2014, 05:20 AM
Replies: 6
Views: 1,515
Posted By gprakhar
L, Stein 2010 Genome Biology...

L, Stein 2010 Genome Biology (http://genomebiology.com/2010/11/5/207) provides convincing arguments for moving to the cloud.
Secondly in my country wide scale adoption of Computational analysis has...
Forum: Bioinformatics 03-21-2014, 05:10 AM
Replies: 6
Views: 1,515
Posted By gprakhar
I am currently reading through the documentation...

I am currently reading through the documentation of CloudBioLinux, it should do the job if I can figure out how to regulate the packages getting installed.
The latest Ubutnu 13.04 based ami is 35...
Forum: Bioinformatics 03-18-2014, 11:29 PM
Replies: 6
Views: 1,515
Posted By gprakhar
Preinstalled Genomic analysis Tools for Cloud Computing

One challenge in harnessing Cloud computing is IT related i.e., installation and testing of bioinformatics tools.
The situation is compounded by the fact that there is no common...
Forum: Bioinformatics 01-07-2014, 01:40 AM
Replies: 366
Views: 182,579
Posted By gprakhar
Adapter Contamination Detection

Hello,

This blog post (pathogenomics.bham.ac.uk/blog/2013/04/adaptor-trim-or-die-experiences-with-nextera-libraries/) is also of relevance here.

I am assembling a Bacterial Genome.
Library...
Forum: Bioinformatics 08-08-2012, 03:24 AM
Replies: 3
Views: 1,121
Posted By gprakhar
Hello, I guess, SNP information from CNV...

Hello,

I guess, SNP information from CNV regions can help in genotyping.
That is, information about the Copy number variation in the different alleles of the sample.

--
pg
Forum: Bioinformatics 07-25-2012, 12:01 AM
Replies: 7
Views: 4,170
Posted By gprakhar
I think the "-genome" is used incorectly, the...

I think the "-genome" is used incorectly, the word "name" should not be there. Only the name of the genome should come after the "-genome" option.

Also the "-chrom" and "-genome" options are...
Forum: Bioinformatics 07-21-2012, 12:57 AM
Replies: 5
Views: 2,987
Posted By gprakhar
Hello, Might be RAM issue, Blast2go uses a...

Hello,

Might be RAM issue, Blast2go uses a lot of memory.
For our node with 96 Gb RAM, we still have to split the blast xml results and then run Blast2Go.

Try spliting the xml input and then...
Forum: Bioinformatics 07-21-2012, 12:54 AM
Replies: 7
Views: 4,170
Posted By gprakhar
Hello, What all commands did you use? ...

Hello,

What all commands did you use?


For us it took,
22 mins to run the CNVnator tool on a single 3.2 GHz Intel I3 processor with a 4GB DDR3 (1333 Mhz), 2TB Western Digital hard disk and...
Forum: Bioinformatics 07-08-2012, 10:46 PM
Replies: 26
Views: 14,564
Posted By gprakhar
Hello, CNVnator is one of the best tools for...

Hello,

CNVnator is one of the best tools for CNV detection, according to my analysis, for a single sample only.
If you have a Tumor normal pair kind of data then FREEC is a good option.

--...
Forum: Bioinformatics 07-08-2012, 10:31 PM
Replies: 1
Views: 2,175
Posted By gprakhar
Hello, This is from the CNVnator manual. ...

Hello,
This is from the CNVnator manual.

********
>>>VISUALIZING SPECIFIED REGIONS

./cnvnator -root file.root [-chrom chr_name1 ...] -view bin_size [-ngc]

Once prompted enter a genomic...
Forum: Bioinformatics 05-27-2012, 10:51 PM
Replies: 14
Views: 4,404
Posted By gprakhar
The Soyabean people do have a custom Repeat...

The Soyabean people do have a custom Repeat Library for it. I got it from here, http://SoyTEdb.org
I use this command,
$RepeatMasker -s -nolow -norna -no_is -gff -lib Glycine_max_TE_lib.fa...
Forum: Bioinformatics 04-20-2012, 01:38 AM
Replies: 40
Views: 18,638
Posted By gprakhar
Hello, This is not a direct answer to your...

Hello,

This is not a direct answer to your question, but there is a tool from the Repeat Masker group.
Its called Repeat Modeler, this tool integrates Repeat Scout, RECON and TRF.
It creates a...
Forum: Bioinformatics 01-12-2012, 03:38 AM
Replies: 2
Views: 2,647
Posted By gprakhar
Hi, Please take a look at these posts, as...

Hi,

Please take a look at these posts, as this topic has been discussed before.

http://seqanswers.com/forums/showthread.php?t=12361
http://seqanswers.com/forums/showthread.php?t=9480
...
Forum: Bioinformatics 01-12-2012, 03:35 AM
Replies: 12
Views: 2,952
Posted By gprakhar
Hello, Did you use the Ensemble pipeline? ...

Hello,

Did you use the Ensemble pipeline?
If yes can you provide a few details!

Regards,
--
pg
Forum: Bioinformatics 01-09-2012, 11:51 PM
Replies: 3
Views: 2,002
Posted By gprakhar
Hi, You could look at, ...

Hi,

You could look at,
http://openwetware.org/wiki/Wikiomics:Repeat_finding#RepeatScout
For analysis.

or

Alternatively I would recommend use Repeat-Modeler...
Forum: Bioinformatics 11-30-2011, 02:44 AM
Replies: 2
Views: 2,187
Posted By gprakhar
Hello, Something wrong with your bam! BTW...

Hello,

Something wrong with your bam!
BTW Is it a bam?

--
pg
Forum: Bioinformatics 11-28-2011, 10:39 PM
Replies: 2
Views: 2,214
Posted By gprakhar
Lightbulb Solved

Hi,

No you can not use the "consensi.fa" file as the final result file.

I just took the top 500 scaffolds from my input file and ran Repeat Modeler on them.
It worked and produced a...
Forum: Bioinformatics 11-27-2011, 11:07 PM
Replies: 2
Views: 2,214
Posted By gprakhar
Hello, Should I use the "consensi.fa" file...

Hello,

Should I use the "consensi.fa" file for further analysis, has the run got over properly?
Can anyone provide an insight?

--
pg
Showing results 1 to 25 of 78

 


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