Forum: Bioinformatics
06-02-2015, 03:30 AM
|
|
Replies: 0
Views: 1,067
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, 01:40 AM
|
|
Replies: 0
Views: 1,585
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, 07:56 AM
|
|
Replies: 4
Views: 3,311
|
|
Forum: Bioinformatics
09-21-2013, 07:58 AM
|
|
Replies: 4
Views: 3,311
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, 10:12 AM
|
|
Replies: 74
Views: 40,526
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, 09:44 AM
|
|
Replies: 8
Views: 14,240
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, 08:58 AM
|
|
Replies: 74
Views: 40,526
|
|
Forum: Bioinformatics
05-28-2013, 02:16 AM
|
|
Replies: 8
Views: 14,240
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, 08:43 AM
|
|
Replies: 8
Views: 14,240
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, 09:34 AM
|
|
Replies: 56
Views: 15,003
|
|
Forum: Bioinformatics
07-21-2012, 08:47 AM
|
|
Replies: 3
Views: 3,056
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, 04:30 AM
|
|
Replies: 1
Views: 3,413
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, 09:48 PM
|
|
Replies: 15
Views: 10,394
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, 09:18 PM
|
|
Replies: 0
Views: 2,150
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, 08:05 AM
|
|
Replies: 65
Views: 19,385
|
|
Forum: Bioinformatics
07-12-2012, 11:34 PM
|
|
Replies: 65
Views: 19,385
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, 09:24 AM
|
|
Replies: 56
Views: 15,003
|
|
Forum: Bioinformatics
06-21-2012, 09:08 AM
|
|
Replies: 56
Views: 15,003
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, 09:50 AM
|
|
Replies: 15
Views: 12,314
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, 09:04 AM
|
|
Replies: 10
Views: 3,779
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
06-02-2012, 11:18 PM
|
|
Replies: 0
Views: 1,851
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, 07:11 PM
|
|
Replies: 0
Views: 1,719
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, 03:38 AM
|
|
Replies: 0
Views: 2,917
|
|
Forum: Bioinformatics
03-22-2012, 09:15 AM
|
|
Replies: 5
Views: 4,591
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, 09:05 AM
|
|
Replies: 10
Views: 3,779
|
