Is there a tool?

Is there a tool that can help me to identify chromosome and coordinate of mutations formatted...

08 September 2015 4,851 2 View

Why do I get a G>A mutation in my sequencing data?

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

Can anyone provide a *.bed file human exome?

To be used in Genome MuSIC.

03 April 2014 222 1 View

Can you suggest a P-value cutoff for a somatic variant call?

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?

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

What should be the minimum depth of coverage for variant call?

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?

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

EdgeR pipeline for a differential expression?

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

VCF compare: Can anyone suggest an appropriate tool?

Job is to find somatic mutation from paired (GATK) VCFs from tumor and normals.

31 December 2013 2,505 2 View

Comparing VCFs for somatic mutations?

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

Is it possible for two human neuronal cell lines to have different gene sequence for the same protein?

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

Genome-wide gene identification protocol ?

Is there any book chapter/book, webpage or research article available to understand genome-wide gene identification?

28 February 2021 8,095 1 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

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

RNA-seq DEGs downstream analysis and reporting in literature?

I used EdgeR to get the list of DEGs (differentially expressed genes) from my liver RNA-seq experiment. I have done the gene overrepresentation and GSEA based pathway analysis. I am currently...

23 February 2021 8,969 1 View

Could you please suggests a tutorial or paper or any other materials to learn multiple gene expression in TCGA and GTEx databases?

I would like to analyze multiple gene expressions in normal and cancer tissue by using the data in the TCGA and GTEx databases. Please suggest a tutorial or paper showing step by step analysis of...

23 February 2021 9,007 3 View

Are there any databases for gene co-expression or expression pattern clustering?

I am currently working on gene clustering based on co-expression pattern in mouse brain. The problem is I do not have some solid way to test my result. Are there any suggestions for databases...

22 February 2021 4,374 3 View

Which CpGs have a significant effect on gene expression?

It is known that methylated CpG around TSS decreases gene expression. However, It is difficult to know exactly which CpG has a greater impact on gene expression. Are there any databases known...

20 February 2021 5,634 3 View

I can detect my protein but the encoding DNA sequence has stop codons within. Should I ignore the stop codons?

I constructed a synthetic DNA library (scFv, VH-VL orientation) with a 3' reporter and 8x histag. I cloned and expressed this gene following which I performed an ELISA. The ELISA results suggested...

19 February 2021 7,006 5 View

Purification of proteins from baculovirus-infected insect cells?

18 February 2021 6,665 6 View

Found that there was a multiple band when amplifiying targeted gene ?

i few days ago amplified specific gene using PCR with specific primers, but there was a multiple band in electrophoregram i found. out of 10 sample amplified, there was multiple band and there was...

18 February 2021 5,131 5 View