35 Questions 157 Answers 0 Followers
Questions related from Navonil De Sarkar
Is there a tool that can help me to identify chromosome and coordinate of mutations formatted...
09 September 2015 4,966 2 View
If you see most of your relevant mutations G>A, what would you infer (generally) other than any sequencing error. Chances of sequencing errors are already addressed. Data generated on Prostate...
08 August 2015 7,281 6 View
To be used in Genome MuSIC.
04 April 2014 324 1 View
Is there any restriction enzyme which can specifically cut a DNA strand sensing either a stretch of 8Cs or 8Gs?
04 April 2014 2,305 0 View
I am using fisher exact test to call for somatic mutation. Now, if I go for any multiple correction, it appears to me as overdone. It is removing almost everything. With, 0.01 cut off on and...
04 April 2014 5,057 3 View
For calling somatic several events could happen. One is LOH. For LOH what should be the minimum depth of coverage in the paired diseased tissue which is homozygous at this locus (blood is a...
03 March 2014 1,872 3 View
What should be the minimum read depth of a minor allele for a reliable variant call? I would be needing some journal reference in that respect. I would like to cite it as a support for the choice...
03 March 2014 3,508 8 View
For a differential expression with CPM, what should be the fold change cutoff for considering the expression deregulated?
02 February 2014 9,316 11 View
Job is to find somatic mutation from paired (GATK) VCFs from tumor and normals.
01 January 2014 2,610 2 View
I need to compare VCFs for somatic mutations (paired samples), including snp, indel and LOH. Is there any tool other than Mutect that I can use?
01 January 2014 918 2 View
Expecting links for technical reports, papers, book link etc
12 December 2013 3,465 5 View
Especially choice of aligner, different cut offs, whether to do duplicate removal cause RNA seq libraries are enzyme cut libraries, minimum depth of coverage for variant calling, rare allele...
12 December 2013 892 7 View
Pipeline using: HT-seq, Dseq
12 December 2013 2,582 0 View
I need some assistance. If you can share a GFF ready file for gencode 19 would also help me.
12 December 2013 6,903 3 View
What does it mean by the term - biological replicates
07 July 2013 6,053 5 View
Head and neck miRNA and mRNA expression deregulation database. Aware of TCGA. Want know about others.
07 July 2013 9,623 2 View
Please share your experiences
07 July 2013 357 1 View
I want to built a synteny map of human with that of Macac. Need suggession, what tool or approach I should take.
06 June 2013 6,152 5 View
Aligner like BWA consider it a straightened reference, starting from 0 and ending at the end coordinate. Now the issue is with the reads which are starting from some tail ending coordinate and...
04 April 2013 2,029 7 View
What should be the platform of your choice, if you are doing somatic mutation study, using ION platform
03 March 2013 7,004 4 View
Should one use mirvana isolated total RNA for their RNA seq project?
03 March 2013 2,724 5 View
Recently got to know about 3 step normalization for RNA seq data, can anyone give me appropriate references for that. 3 step nor malization are at RPKM level, between gene level and may be within...
03 March 2013 9,515 5 View
Any information about it's function, expression, association with some drugs, etc.
03 March 2013 3,310 1 View
I need a suggession for a good RNA isolation protocol from Serum/Plasma. Looking for any kit name of any modification of protocol etc
02 February 2013 2,908 11 View
Please suggest a good assembly pipeline for an ION torrent data for a bacteria. I have tried MIRA3 where the largest contig size is 1.1 mb, but N50 is some where around 7000 only. Tried to blast...
01 January 2013 7,387 10 View
I want to see differential expression, novel transcript, novel splice variants, and some information about NON coding RNA s too. Should I enrich my sample with poly Ts then, or just go for...
01 January 2013 9,890 8 View
If I wish to do whole methylome study of human what should be my chipseq platform of choice and why?
01 January 2013 5,828 1 View
Is there any direct method of studing methylation. Is there any modified nucleotide which can bind specifically to methylated Nucleotide? Do not want to do bisulfide sequencing. Is there any other...
01 January 2013 569 2 View
I have sequenced a bacterial 16S rRNA coding region using capillary sequencing and then got the De-Novo assembly (DNA sequence) of the same bacteria (same pure culture). After a blast search I...
12 December 2012 9,248 11 View
Num. reads assembled: 1669184 Avg. total coverage: 16.60 Number of contigs: 13991 Largest contig: 112360 N50 contig size: 1171 that is the summary I got out of a de novo assembly (ion torrent...
12 December 2012 4,582 13 View
For cancer still I may understand the need ( to capture the variation due to multiple clone), but why it is needed for other disease.
10 October 2012 782 7 View
I had 2 runs from the same library at some NGS platform (intentionally not mentioning the name of the platform) and I have ended up with some strange findings. In my second run I found some extra...
10 October 2012 720 24 View
For Ultra High Resolution Agarose Gels (Invitrogen), do you need to electrophorese the gel for longer than you normally would? I have not done it before. Would the results be similar or comparable...
10 October 2012 2,656 4 View
Option from other databases are also equally welcome
09 September 2012 9,234 3 View
I need the souce of Publicly available Cardio vascular disease microarray data. Please assist me on this
09 September 2012 2,098 2 View
