Pipeline using: HT-seq, Dseq
Is there a tool that can help me to identify chromosome and coordinate of mutations formatted...
08 September 2015 4,851 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...
07 August 2015 7,176 6 View
To be used in Genome MuSIC.
03 April 2014 222 1 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...
03 April 2014 4,932 3 View
Is there any restriction enzyme which can specifically cut a DNA strand sensing either a stretch of 8Cs or 8Gs?
03 April 2014 2,208 0 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...
02 March 2014 1,762 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...
02 March 2014 3,384 8 View
For a differential expression with CPM, what should be the fold change cutoff for considering the expression deregulated?
01 February 2014 9,151 11 View
Job is to find somatic mutation from paired (GATK) VCFs from tumor and normals.
31 December 2013 2,505 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?
31 December 2013 819 2 View
I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance
03 March 2021 3,568 1 View
Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue
02 March 2021 5,433 5 View
I am looking at the ATP1A2 (Sodium/Potassium ATPase alpha subunit 2) in two human neuronal cell lines. Expression levels of this protein seems to be almost equal when detected by one antibody....
01 March 2021 3,607 3 View
I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...
28 February 2021 4,949 3 View
Is there any book chapter/book, webpage or research article available to understand genome-wide gene identification?
28 February 2021 8,095 1 View
Hi everybody In the ped format for genotype, alleles of any SNP are represented by two columns (one for each allele, separated by a space). Is a column sufficient for the haplotype to...
27 February 2021 1,965 1 View
I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...
27 February 2021 356 6 View
Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...
27 February 2021 9,233 3 View
I performed site directed mutagenesis, transformation, and then I sent out plasmids for Sanger sequencing and found out that there is extension of DNA just before the stop codon. I am not sure...
27 February 2021 547 3 View
Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...
25 February 2021 6,969 3 View
