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Forum: Bioinformatics 12-03-2016, 07:07 PM
Replies: 3
Views: 2,061
Posted By BhariD
how to become a reviewer for Bioinformatics journals?

I would really like to offer peer-reviewing for the Bioinformatics/computational biology/cancer research journal or conferences. Anyone here have suggestions on how to become a reviewer for such...
Forum: Bioinformatics 11-30-2016, 08:15 PM
Replies: 3
Views: 1,923
Posted By BhariD
With differentially expressed genes, I meant to...

With differentially expressed genes, I meant to say genes that are over-expressed or under-expressed within a single experimental group consisting of more than one replicates. There is no second...
Forum: Bioinformatics 11-28-2016, 07:14 AM
Replies: 3
Views: 1,923
Posted By BhariD
How to identify differentially expressed genes within a single sample group?

What are the reasonable ways to identify differentially expressed genes within a Single sample group consisting of 5 replicates with RNA-seq data? There is no second or other group to compare. ...
Forum: Bioinformatics 04-30-2015, 01:56 PM
Replies: 0
Views: 919
Posted By BhariD
Varscan2 multi-variant samples VCF output with empty sample call FORMAT column?

Hi

I have Varscan2 generated multi-sample (three samples total) variant VCF file.
I ran Varscan2 on default settings.

For few variants, there is no variant call FORMAT string (e.g.,...
Forum: Bioinformatics 01-14-2014, 01:40 PM
Replies: 62
Views: 25,669
Posted By BhariD
skewer: A fast and sensitive adapter trimmer for paired-end reads

Also, what is the base quality value threshold used by the tool to be considered as a mismatch? in "3) The program only provides a parameter of error ratio (by -r) and detect the most possible...
Forum: Bioinformatics 01-14-2014, 12:00 PM
Replies: 62
Views: 25,669
Posted By BhariD
Thank you for your prompt response! I am...

Thank you for your prompt response!

I am sorry, I couldn't quite get the "In current implementation, adapter sequence longer than 64 nt will be cut to 64 nt before processing"? I don't think I...
Forum: Bioinformatics 01-14-2014, 06:10 AM
Replies: 62
Views: 25,669
Posted By BhariD
Hi, I have to trim full-length adapter...

Hi,

I have to trim full-length adapter sequences with zero number of mismatches. I do not want to trim reads on any other criteria at this point.

I am using the following command line:...
Forum: Bioinformatics 11-08-2013, 02:27 AM
Replies: 2
Views: 1,019
Posted By BhariD
targeted resequencing data analysis tool

Hi,

What tool would you recommend for aligning/assembling data obtained from targeted sequencing (Illumina paired-end) of a gene of interest (species is homo sapiens) from different samples?
...
Forum: Sample Prep / Library Generation 08-11-2013, 02:44 PM
Replies: 8
Views: 8,719
Posted By BhariD
presence of mtDNA in RNA-seq data?

I have similar experience with my human RNA-seq data for 6 samples. I am also finding lot of mt sequence in the libraries (~1% to 5%).

I would like to take this opportunity to ask a question. What...
Forum: Sample Prep / Library Generation 07-21-2013, 06:20 PM
Replies: 1
Views: 1,609
Posted By BhariD
RNA-seq contamination with human mitochondrial sequence?

Can we expect human mitochondrial sequence in Human RNA-seq library? I mean does the presence of mitochondrial sequence in RNA-seq data stands biological significance or likely a result of...
Forum: RNA Sequencing 07-21-2013, 05:57 PM
Replies: 0
Views: 1,802
Posted By BhariD
RNA-seq contamination with human mitochondrial sequence?

Can we expect human mitochondrial sequence in Human RNA-seq library? I mean does the presence of mitochondrial sequence in RNA-seq data stands biological significance or likely a result of...
Forum: Bioinformatics 07-14-2013, 03:18 PM
Replies: 2
Views: 2,620
Posted By BhariD
over-represented mitochondrial sequences in the RNA-seq data

I have Illumina RNA-seq data. I have been finding a lot of overrepresented sequences in the library (>0.1% of total, some are even 0.3%) in all the samples I have.

These over-represented sequences...
Forum: Bioinformatics 05-16-2013, 01:55 PM
Replies: 0
Views: 1,661
Posted By BhariD
How and what to use to filter out any known SNPs (with rs#) from the vcf file?

Given a vcf file, is there a feature in SNP analysis package to filter out known SNPs (SNPs with rs# associated with)? If so, how is it done? Is it simply the concordance between the variant call in...
Forum: Bioinformatics 05-07-2013, 10:50 AM
Replies: 0
Views: 4,177
Posted By BhariD
how to compute Minor Allele Frequency for a variant call?

I am interested in computing the minor allele frequency (MAF) for each variant or SNP call in the RNA-seq data obtained from Varscan calling method. Is it as simple as the fraction of number of...
Forum: Bioinformatics 04-22-2013, 07:19 AM
Replies: 1
Views: 3,264
Posted By BhariD
criteria for filtering SNPs

Hi,

I have variant (SNP) calls made from the GATK (vcf format). I have a tumor data-sets (No normal data-set). I have filtered out the SNPs that are present in the public domain such as dbSNP as I...
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