Can anyone help me with 'insertion size' when running tophat or other RNA-seq reads aligners?

02 March 2015 2,771 3 View

Any suggestions about some tools for CNV calling analysis on whole Exome sequencing data?

I am doing some CNV calling analysis on whole Exome sequencing data. Can anyone recommend some tools for CNV on WES data? I have done some literature search, and VarScan2 is one of tools suitable...

02 March 2015 5,848 3 View

Are there tools that can simulate gene fusion RNA-Seq reads?

I have two questions regarding gene fusion: 1) are there existing tools that can simulate gene fusion rna-seq reads? 2) how to determine the fusion gene allele frequency based on rna-seq reads? by...

01 February 2015 5,835 2 View

How to define syntenic blocks between human and mouse?

Is there such a file in which, the human-mouse syntenic regions are listed one to one, correspondingly? I need all the syntenic regions between human and mouse. If there is no such file, how can I...

09 October 2013 4,322 4 View

Large difference between two 'biological replicates' (Sequencing data)

I have run some genome-wide comparison of methylomes from two biological replicates. The results are showing there are many Differentially Methylated Regions (DMRs) between these two samples. I...

01 February 2013 7,949 0 View

My gel extraction did not go well...

I am working on MRE-library construction, which basically requires cutting the gel slices of 220-600bp lengths. I attached my gel picture here, it was after PCR amplification and before gel...

31 December 2012 3,610 6 View

how does 'paired ended' MeDIP-seq work?

My basic understanding of 'paired ended' sequencing is that it adds nucleotides to both ends of the fragment that's to be sequenced. My questions are: for MeDIP-seq, usually how many nucleotides...

08 September 2012 3,536 0 View

Coverage of CpG sites and Saturation analysis of MeDIP-seq & MRE-seq data.

1) How to calculate the coverage of CpG sites of the MeDIP & MRE data? (can anyone give me some details on this)? 2) How to do saturation analysis? I know what saturation analysis mean and I know...

07 August 2012 5,430 4 View

BS-PCR - all runs failed

There can be different reasons which could have caused the BS-PCR to not work, for now, what I can think of include: 1) The annealing temperature setting in the thermocycler: the Tm of my...

06 July 2012 9,507 7 View

How do I increase the yield of my PCR product?

Hello, We would like to increase the yield of our PCR product. We are running a series of PCR reactions that is targeting ~1.1kb sequence. We begin each reaction with ~400pg of template DNA...

02 March 2021 4,029 3 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

How to address this issue in the analysis of Real-Time PCR results?

To dear Researchers, I was analyzing a series of concentration for estimation of Real-Time PCR efficiency. The concentration was 1:10. I used MS-excel to evaluate Slope. The result of slope was -8...

01 March 2021 8,683 4 View

No title

Does anyone have the experience of using Taq Man probes in the QIAGEN Rotar- Gene qPCR machine?

01 March 2021 5,311 1 View

MiRNA qpcr problem?

Dear All, mirna primer showing some problem in the melting curve? any idea why? As attached is the melting curve. The forward sequence is obtained from miRBase and reverse primer is universal.

28 February 2021 5,008 4 View

Runs of nucleotides in Sanger sequencing?

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

Can thermal cycler machines be problematic during PCR?

Hi, my question is about the heating of thermal cycler machines and I hope some of you had experienced a similar thing previously. There are two thermal cycler machines in the lab(BioRad) and for...

26 February 2021 4,777 4 View

Calculating volume of DNA required from DNA concentration?

Hi I am a bit confused. They are asking me to find out the volume of DNA required in ul (a total of 30-100 ng for genomic DNA) from the DNA concentration in the nanodrop reading which was 404.8...

26 February 2021 5,029 2 View

Has anyone used the Illumina ITS1 primer sets?

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

Why do the PCR bands from the cDNA templates (extraction from the cell after transfection) show different size from the band of the plasmid template?

After transfection with the plasmid ( linearized ) and subcloning of the cell lines, RNA was extracted from the cell and then reverse transcripted to cDNA. When PCR reactions were run to verify...

25 February 2021 5,712 3 View