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Forum: Illumina/Solexa 05-30-2016, 10:36 PM
Replies: 1
Views: 1,989
Posted By Nilaksha
Smile Custom oligo providers for Illumina Library Preparation

Hey,

We have a miseq and presently we only rely on Illumina provided library preparation reagents. (Trusight One, Trusight Cancer etc).
Does anyone use custom oligos with a miseq synthesized by...
Forum: Bioinformatics 04-22-2015, 03:08 AM
Replies: 1
Views: 1,882
Posted By Nilaksha
snpeff canonical transcript annotations: multiple annotations problem

Hi,
I'm using snpEff in my exome sequencing pipeline and I use -canon option to get only the canonical transcripts annotated for a particular variant. But eventhough I'm using the option, I can see...
Forum: Bioinformatics 10-16-2014, 08:46 PM
Replies: 7
Views: 8,139
Posted By Nilaksha
Just a reminder : you can use java -Xmx[your...

Just a reminder : you can use java -Xmx[your memory]G to get the maximum use of it. In your case you can use
java -Xmx60G -jar /picard-tools/ ... (Leave 4GB for background processes)
Forum: Bioinformatics 08-05-2014, 01:05 AM
Replies: 2
Views: 1,800
Posted By Nilaksha
HLA haplotype analysis

Hi, I have a set of HLA variants from a case control study annotated in tabulated files. I thought of analyzing them with plink and after a hard work, I tried to convert my raw data to plink...
Forum: Bioinformatics 06-05-2014, 10:25 PM
Replies: 2
Views: 1,352
Posted By Nilaksha
Transcript details from exome sequencing!!!

I know my question is silly, but after seeing the same thing on so many places I had to ask this question.
Is there any possibility to predict the specific transcript (obtained by alternative...
Forum: Genomic Resequencing 05-05-2014, 08:15 PM
Replies: 2
Views: 4,493
Posted By Nilaksha
Thanks for the valuable info. Much appreciated.

Thanks for the valuable info. Much appreciated.
Forum: Genomic Resequencing 05-04-2014, 10:15 PM
Replies: 2
Views: 4,493
Posted By Nilaksha
CNV and INDEL calling

Hello,

I have been able to successfully develop a pipeline for SNP calling from exome sequence data and keen to look for indels and CNVs as well. I have heard that dindel is good for indel calling...
Forum: Bioinformatics 04-08-2014, 07:44 PM
Replies: 5
Views: 2,906
Posted By Nilaksha
Hey thanks a lot, I guess I can work it out...

Hey thanks a lot,

I guess I can work it out now/ :)
Forum: Bioinformatics 04-07-2014, 08:01 PM
Replies: 9
Views: 4,874
Posted By Nilaksha
Did you use picard tools at any of the steps in...

Did you use picard tools at any of the steps in your workflow?
Forum: Bioinformatics 04-06-2014, 09:56 PM
Replies: 5
Views: 2,906
Posted By Nilaksha
I tried importing csv file obtained by...

I tried importing csv file obtained by table_annovar.pl script of ANNOVAR to IGV but had no luck. Is there any particular method that worked for you ?
Forum: Metagenomics 03-31-2014, 08:33 PM
Replies: 3
Views: 5,005
Posted By Nilaksha
Thanks I will look into that. :)

Thanks I will look into that. :)
Forum: Metagenomics 03-30-2014, 11:38 PM
Replies: 3
Views: 5,005
Posted By Nilaksha
BLAST comparison of 16S rRNA against the SILVA database

I'm currently running metagenomics pipeline through galaxy, and at the taxonomic mapping step I use ncbi blast+ wrappers to blast against a locally installed nt database. But ncbi nt database...
Forum: Bioinformatics 03-24-2014, 11:17 PM
Replies: 5
Views: 2,906
Posted By Nilaksha
Visualize variants annotated with ANNOVAR

Hey all,

I'm developing a pipeline for NGS data analysis. I'm pretty much ok with the steps up to variant calling (I'm using GATK for that) and then I use the already built VCF file to convert it...
Forum: Bioinformatics 03-21-2014, 01:59 AM
Replies: 1
Views: 923
Posted By Nilaksha
Time consumption for a Metagenomic Analysis

Hi all,

I'm a new comer to bioinformatics and have developed a pipeline to do metagenomic analysis using Galaxy, and currently running a fasta file of 4mb, (around 4000sequences). It seems like...
Forum: Introductions 03-18-2014, 01:18 AM
Replies: 1
Views: 1,200
Posted By Nilaksha
Majority of the open source bioinformatics tools...

Majority of the open source bioinformatics tools are intended to be used on a unix based system. They do not contain executable files (.exe). To 'install' the softwares you need to 'build' them via...
Forum: Ion Torrent 03-17-2014, 07:37 PM
Replies: 2
Views: 3,804
Posted By Nilaksha
Thank you very much for the valuable information....

Thank you very much for the valuable information. I checked AllSeq, and it is very informative.
I will go through the site further and ask you if I get any doubts.

Thanking you,
Nilaksha.
Forum: Ion Torrent 03-16-2014, 11:48 PM
Replies: 2
Views: 3,804
Posted By Nilaksha
Human Exome Sequencing using Ion torrent PGM

As the web page of Life technologies said, Ion torrent PGM is for small genomes and targeted gene expressions while the Ion proton is for human genomes and exomes. Yet, I came across that ion torrent...
Forum: Bioinformatics 03-12-2014, 08:24 PM
Replies: 2
Views: 1,414
Posted By Nilaksha
Thanks a lot for the answer. I will read up more...

Thanks a lot for the answer. I will read up more on that and let you know the progress :)
Forum: Bioinformatics 03-12-2014, 01:48 AM
Replies: 2
Views: 1,414
Posted By Nilaksha
Validating and Evaluating the Quality of an NGS pipeline

Hello all, I'm a novice bioinformatician and have developed a NGS analysis pipeline majorly for SNP calling. I would like to evaluate the accuracy of my pipeline either against a set of genotyped ...
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