If I wish to do whole methylome study of human what should be my chipseq platform of choice and why?
Suggessions please
Is there a tool that can help me to identify chromosome and coordinate of mutations formatted...
08 September 2015 4,995 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 7,324 6 View
To be used in Genome MuSIC.
03 April 2014 355 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 5,085 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 2,334 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 1,902 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 3,539 8 View
For a differential expression with CPM, what should be the fold change cutoff for considering the expression deregulated?
01 February 2014 9,402 11 View
Job is to find somatic mutation from paired (GATK) VCFs from tumor and normals.
31 December 2013 2,645 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 955 2 View
I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?
11 August 2024 5,138 1 View
I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...
08 August 2024 4,645 2 View
After performing symmetric PCR, PCR purification was performed. Afterwards, asymmetric PCR was performed using the PCR purification product as a template, but no ssDNA band was confirmed in the...
08 August 2024 1,668 3 View
I'm trying to find a DNA extraction method for fungi that does not require equipment and heating. Is there anyone who can suggest an alternative option? Thank you
08 August 2024 4,733 2 View
I want to introduce a point mutation (change in one nucleotide) into my gene of interest (DNA binding domain) I have designed primers as recommended on the Data sheet of the kit : -Both primers...
05 August 2024 9,059 3 View
I aim to be as skeptical as possible regarding whether a pair of orthologous genes results in the same phenotype in their different but related bacterial organisms under similar environmental...
05 August 2024 6,787 4 View
I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...
01 August 2024 2,079 0 View
I am currently working on a project involving liposomes and need to determine the maximum volume of siRNA that can be added to a 2.5 mL liposome solution with a total lipid concentration of 10...
30 July 2024 6,420 1 View
I am looking for software to help analyze SELEX NGS data, including alignment, sequence enrichment, and other related tasks. Can anyone recommend suitable tools or software? Best wishes, Waleed
30 July 2024 1,061 5 View
PeptiCloud (www.pepticloud.com) is a bioinformatic platform that allows researchers to organize and share their data for their projects as well as collaborate with others in one place. Through...
28 July 2024 4,762 2 View