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Search: Posts Made By: vishnuamaram
Forum: Bioinformatics 06-18-2014, 01:42 AM
Replies: 14
Views: 5,302
Posted By vishnuamaram
That's a great news from alpha. I do have a...

That's a great news from alpha.

I do have a suggestion, I think as the process goes out of memory and your RAM size is less (64gb). Try creating a tmp folder in your server hard drive and give...
Forum: Bioinformatics 06-18-2014, 01:33 AM
Replies: 3
Views: 2,798
Posted By vishnuamaram
hey anusha, there is no error in general...

hey anusha,

there is no error in general while using samtools index, the command line is very simple. let us know what command r u using.

Cross verify whether ur previous steps of samtools...
Forum: Introductions 05-26-2014, 01:55 AM
Replies: 1
Views: 1,616
Posted By vishnuamaram
yes, of course you are welcome to the group....

yes, of course you are welcome to the group. please keep posted your queries, we discuss. :)
Forum: Bioinformatics 02-26-2014, 05:30 AM
Replies: 18
Views: 5,125
Posted By vishnuamaram
Hey Vishal & Braj, Looks like you guys are...

Hey Vishal & Braj,

Looks like you guys are experts in using conifer by now.

I am newbie to bioinfo as well to using NGS & conifer.

Some how, i am learning & working on the stuff.

I was ...
Forum: Bioinformatics 02-18-2014, 12:52 AM
Replies: 5
Views: 2,830
Posted By vishnuamaram
Hey KatrinSameith, Try using FASTXTOOLKIT,...

Hey KatrinSameith,

Try using FASTXTOOLKIT, with this you can specifically trim.
Forum: RNA Sequencing 02-18-2014, 12:50 AM
Replies: 4
Views: 2,249
Posted By vishnuamaram
@ Jeremy : For super0925: The pipeline...

@ Jeremy :

For super0925:

The pipeline looks absolutely perfect for RNAseq analysis in general.
I am not very sure of it using for Ion-proton.

Any how, why dont you give a try of using the...
Forum: Bioinformatics 02-18-2014, 12:44 AM
Replies: 3
Views: 771
Posted By vishnuamaram
Hi pic79, Are the three lanes consist of...

Hi pic79,

Are the three lanes consist of data of same sample.

(1) What is your data mainly. DNA,RNA, small RNA.
(2) Which organism
(3) Consider all options of having a reference genome...
Forum: Clinical Sequencing 12-26-2013, 10:43 AM
Replies: 4
Views: 11,948
Posted By vishnuamaram
Alzheimer's disease-gene database list

Hello All,

I would like to know about any databases if exist which has the entire list of genes implicated in alzheimer's disease (AD).

I know alzgene. but it doesn't has detailed list in it. ...
Forum: Bioinformatics 12-15-2013, 02:45 AM
Replies: 8
Views: 10,783
Posted By vishnuamaram
Hey yl01 & jjmmi, I hope you guys are...

Hey yl01 & jjmmi,

I hope you guys are experts in NGS,especially exome sequencing by now.

I am a kind of amateur and little expert, did part of analysis of my exome data.

This is what i...
Forum: Bioinformatics 12-15-2013, 02:41 AM
Replies: 8
Views: 10,783
Posted By vishnuamaram
Hey yl01 & jjmmi, I hope you guys are...

Hey yl01 & jjmmi,

I hope you guys are experts in NGS,especially exome sequencing by now.

I am a kind of amateur and little expert, did part of analysis of my exome data.

This is what i...
Forum: Bioinformatics 10-29-2013, 05:33 AM
Replies: 3
Views: 1,741
Posted By vishnuamaram
Hey Splinter479, What is your goal of...

Hey Splinter479,

What is your goal of simulating Illumina paired end reads and the purpose of your experiment. Is it sensible to follow this approach.

Regards,
Vishnu.
Forum: Bioinformatics 10-29-2013, 04:08 AM
Replies: 1
Views: 1,594
Posted By vishnuamaram
Hey keerthi, This is Vishnu, involved in...

Hey keerthi,

This is Vishnu, involved in human whole genome analysis for SNPs

My pipeline steps are fine starting with FASTC-bwa-samtools-picard-GATK,where i get errors at GATK indel...
Forum: Bioinformatics 10-29-2013, 04:04 AM
Replies: 2
Views: 1,368
Posted By vishnuamaram
Hey medalofhonour, You may do deleting the ...

Hey medalofhonour,

You may do deleting the chrUn and other files which you dont need and concatenate chr 1-22,x,y and m for further alignment.
Forum: Genomic Resequencing 10-08-2013, 10:13 PM
Replies: 8
Views: 3,203
Posted By vishnuamaram
Hey whataBamBam, I had got your responses on...

Hey whataBamBam,

I had got your responses on other thread too.

Actually, i didnt generate interval file,

My question is how to generate an interval file.

Kindly help me in generating...
Forum: Bioinformatics 10-05-2013, 11:03 AM
Replies: 6
Views: 5,277
Posted By vishnuamaram
Hey persorrels, If i was in your place, i...

Hey persorrels,

If i was in your place, i proceed this way.

I suggest you trim the first 4 bases and run FASTQC on the trimmed file and checked the QC chart.

--> If you see the mean quality-...
Forum: Bioinformatics 10-04-2013, 09:27 AM
Replies: 6
Views: 5,277
Posted By vishnuamaram
Hey persorrels, what is the organism you...

Hey persorrels,

what is the organism you have sequenced, what is the coverage.

how much is the data size. how many reads does your data have ?

why are you seeing individual reads.
...
Forum: Bioinformatics 10-03-2013, 10:55 PM
Replies: 6
Views: 5,277
Posted By vishnuamaram
Hey persorrels, It looks like your approach...

Hey persorrels,

It looks like your approach of trimming the bases and discarding reads is not appropriate.

Illumina gives more or less good quality reads except at the 1st 3-4 base positions...
Forum: Bioinformatics 10-03-2013, 10:47 PM
Replies: 4
Views: 3,687
Posted By vishnuamaram
Hey Arkilis, Geneious is a commercial tool....

Hey Arkilis,

Geneious is a commercial tool. So, i dont think much people use it.

But, the option parameters are more or less same in all available variant calling tools.

Say, for example...
Forum: Bioinformatics 10-02-2013, 10:20 PM
Replies: 15
Views: 7,452
Posted By vishnuamaram
Hey whatabambam, this is the cd i used:- ...

Hey whatabambam,

this is the cd i used:-
java -Xmx30g -jar GenomeAnalysisTK-2.6-5-gba531bd/GenomeAnalysisTK.jar -T IndelRealigner \ -R REF_GENOME_hg19/hg19_karyotypic.fa -I...
Forum: Bioinformatics 10-02-2013, 05:45 AM
Replies: 15
Views: 7,452
Posted By vishnuamaram
Hey guys, (kennels, whatabambam) Kindly any...

Hey guys, (kennels, whatabambam)

Kindly any of you respond and let me know,

what are the proper commands to be used for GATK- indel realigner, BQSR and variant calling.

When ever i run a...
Forum: Bioinformatics 10-02-2013, 05:02 AM
Replies: 3
Views: 3,243
Posted By vishnuamaram
Hey Ire1234, May be that will be using the...

Hey Ire1234,

May be that will be using the space of tmp directory while running this command.

first create a mimic tmp directory in the hard disk and
try to include java ...
Forum: Genomic Resequencing 10-02-2013, 04:43 AM
Replies: 8
Views: 3,203
Posted By vishnuamaram
Hi sheenams, Thank you very much. I had...

Hi sheenams,

Thank you very much.

I had tried using targetIntervals, but stil again it throws error as follows

##### ERROR MESSAGE: Couldn't read file...
Forum: Introductions 10-02-2013, 04:26 AM
Replies: 5
Views: 2,195
Posted By vishnuamaram
Hey guys, Welcome to the NGS analysis world....

Hey guys,

Welcome to the NGS analysis world.
Your first step with any FASTQ sequence file should be to check the quality using tools like say

FASTQC from Babraham Institute. ...
Forum: Bioinformatics 09-23-2013, 05:31 AM
Replies: 24
Views: 20,886
Posted By vishnuamaram
Hey guys, Truly use...

Hey guys,

Truly use VALIDATION_STRINGENCY=LENIENT OR SILENT. when u run most of the picard commands.

That will definitely help. I am experiencing it personally.

Good luck ahead to all NGS...
Forum: Genomic Resequencing 09-09-2013, 09:50 PM
Replies: 8
Views: 3,203
Posted By vishnuamaram
GATK-usage-ERROR-Helpreg

Hi Seqanswers community,


I am doing human whole genome sequence analysis, of the data obtained Illumina Hiseq 2000.

This is the pipeline i followed & get errors in using GATK


a) BWA...
Showing results 1 to 25 of 42

 


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