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Search: Posts Made By: pravee1216
Forum: Bioinformatics 06-02-2015, 04:30 AM
Replies: 0
Views: 966
Posted By pravee1216
Detect cleavage sites in bacterial RNAseq data

Dear Folks -
Do you have experience / expertise with - any bioinformatics protocols for detecting the cleavage sites in RNA using whole transcriptome (RNAseq) data of bacteria? The total RNA of...
Forum: RNA Sequencing 10-13-2014, 02:40 AM
Replies: 0
Views: 1,476
Posted By pravee1216
common mRNA isolation kit for bacteria and fungi

Dear Folks,
Just curious to know about any mRNA isolation protocol available today that works for both bacterial and fungi. I have an NGS experiment where the total RNA needs to isolated from a...
Forum: Bioinformatics 09-22-2013, 08:56 AM
Replies: 4
Views: 3,168
Posted By pravee1216
Thanks, but I recently came through an article:...

Thanks, but I recently came through an article: Transcriptome analysis of two buffalograss cultivars (M Wachholtz et al) discussed the same scenario. Here are some key text from this article:-
...
Forum: Bioinformatics 09-21-2013, 08:58 AM
Replies: 4
Views: 3,168
Posted By pravee1216
Merging transcripts of two genotypes

I have one question related to constructing transcriptome using de novo of two genotypes for expression studies.

I have two conditions - treated and control samples - from two genotypes of a...
Forum: Bioinformatics 05-30-2013, 11:12 AM
Replies: 74
Views: 39,108
Posted By pravee1216
Thanks, E. It's a good article. Thanks for...

Thanks, E. It's a good article.

Thanks for reminding me the RABT option. That created 400 times bigger transcripts.gtf files by cufflinks.

What is the suggested value of --min-isoform-fraction...
Forum: Bioinformatics 05-30-2013, 10:44 AM
Replies: 8
Views: 14,099
Posted By pravee1216
Actually, the amount of ready data (5Kb insert)...

Actually, the amount of ready data (5Kb insert) at this moment is ~80x, however the plan is to go for another long insert library (10Kb) sequencing at ~60-70x.

Do you know any >2GB genome assembly...
Forum: Bioinformatics 05-29-2013, 09:58 AM
Replies: 74
Views: 39,108
Posted By pravee1216
Based on experience, can anyone suggest a better...

Based on experience, can anyone suggest a better tool for studying spliced isoform expression between two conditions (using single-end data without replicates)? Setting up Alexa-seq is very complex...
Forum: Bioinformatics 05-28-2013, 03:16 AM
Replies: 8
Views: 14,099
Posted By pravee1216
Thanks for the details, flxlex I have PacBio...

Thanks for the details, flxlex

I have PacBio short and long data with >130x coverage each. The coverage of Illumina PE and 454 MP data are >150x.

Do you think the phase-1 stages necessary?...
Forum: Bioinformatics 05-27-2013, 09:43 AM
Replies: 8
Views: 14,099
Posted By pravee1216
Assembly of a 3Gb mammalian genome

Dear Friends,
I was working on the assembly of a 3Gb mammalian genome using next-gen data from multiple platforms. I have data from Illumina HiSEQ (PE, ~160x sequence depth) with multiple library...
Forum: Bioinformatics 09-11-2012, 10:34 AM
Replies: 56
Views: 14,264
Posted By pravee1216
Hi Chandra, Nice to see the update. Does...

Hi Chandra,

Nice to see the update. Does this version support or run on a cluster system? Do you have any plan to release it?

Thanks

Praveen.
Forum: Bioinformatics 07-21-2012, 09:47 AM
Replies: 3
Views: 2,875
Posted By pravee1216
Running Unified Genotyper on individual samples...

Running Unified Genotyper on individual samples and identifying true somatic calls would be difficult as you may require a statistical score/probability value and variant_allele_frequency (VAF) to...
Forum: Bioinformatics 07-19-2012, 05:30 AM
Replies: 1
Views: 3,266
Posted By pravee1216
Summary of multi-sample VCF

All,

Does anyone know any tool that can summarize the variants in a multi-sample VCF file? I would require a table format summary of variants that shows:

a) #novel
b) #dbSNP
c) dbSNP_%
d)...
Forum: Bioinformatics 07-18-2012, 10:48 PM
Replies: 15
Views: 10,002
Posted By pravee1216
platform independent?

Good news!!

Couple of questions:

a) Does Strelka support alignment files from Roche 454/FLX sequencing reads? or Is it designed mainly for Illumina data?

b) How does it handle calls at...
Forum: Bioinformatics 07-15-2012, 10:18 PM
Replies: 0
Views: 1,981
Posted By pravee1216
Indexing of bacterial genome for bwa-sw/Bowtie2

I would be interested in mapping reads to complete bacterial genomes using bwa-sw or Bowtie2. But I'm unable to index the complete genome file (single FASTA with all bacterial genomes from NCBI)...
Forum: Bioinformatics 07-15-2012, 09:05 AM
Replies: 65
Views: 18,385
Posted By pravee1216
has anyone experience this problem?

Has anyone experience the above problem?
Forum: Bioinformatics 07-13-2012, 12:34 AM
Replies: 65
Views: 18,385
Posted By pravee1216
Another strange behavior of NGSrich

All,

I'm struggling for almost a week in executing NGSrich v0.7.7 on an aligned BAM file with SureSelect All Exon V2 target bed file. The sorted/indexed BAM file (aligned using BWA against hg19...
Forum: Bioinformatics 06-24-2012, 10:24 AM
Replies: 56
Views: 14,264
Posted By pravee1216
Sounds good. When would it be available to us? Is...

Sounds good. When would it be available to us? Is this version capable to run on a server system?

Thanks for the initiative of building this version

Praveen.
Forum: Bioinformatics 06-21-2012, 10:08 AM
Replies: 56
Views: 14,264
Posted By pravee1216
Installation on cluster

Hi Chandra,

One quick question. Do you provide an installer to setup and run PathSeq on a local cluster/server? It would be great if we have one. BWA based alignment against other genomic...
Forum: Bioinformatics 06-16-2012, 10:50 AM
Replies: 15
Views: 11,895
Posted By pravee1216
ExpressionBarPlot in cummeRbund

BTW, what do the error bars in the expressionBar plot represent for each gene? I don't find any documentation specific to this? Any help?
Forum: Bioinformatics 06-07-2012, 10:04 AM
Replies: 10
Views: 3,584
Posted By pravee1216
I contacted the team who published the nature...

I contacted the team who published the nature publication. They used an in-house tool to produce these plots. They're in the process of publishing it, hence under manuscript review. Meantime, I asked...
Forum: Bioinformatics 06-03-2012, 12:18 AM
Replies: 0
Views: 1,705
Posted By pravee1216
Discovery of viral pathogen from IonTorrent data

All,

I'm seeking your advice and suggestions to identify the viral genome from viral-infected patient sample sequenced on IonTorrent. A totol 0.34 million reads of length 5-202bp DNA reads was...
Forum: Bioinformatics 05-17-2012, 08:11 PM
Replies: 0
Views: 1,568
Posted By pravee1216
Tool for analyzing low-coverage human data

All,

Can anyone suggest me good mapping tool(s) for aligning low-coverage SOLiD human data? My objective is to identify variants and the coverage is ~3x (after filtering). I tried using...
Forum: Bioinformatics 05-12-2012, 04:38 AM
Replies: 0
Views: 2,723
Posted By pravee1216
Somatic mutation profiling from 454 tumor-normal paired data

Hello All,

I would be interested to do somatic mutation discovery from 454 tumor-normal paired data. Since I have handled many projects on Illumina and SOLiD project on the same requirements, but...
Forum: Bioinformatics 03-22-2012, 10:15 AM
Replies: 5
Views: 4,381
Posted By pravee1216
I don't think so, because duplicate removal...

I don't think so, because duplicate removal doesn't mean that reads mapped to multiple locations are eliminated. Both are two different concepts. why I am saying this because even if you dedup reads,...
Forum: Bioinformatics 03-22-2012, 10:05 AM
Replies: 10
Views: 3,584
Posted By pravee1216
Not yet, I think I should try that.

Not yet, I think I should try that.
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