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Questions related from Jia Zhou
I have paired-end reads, the reads length is 150bp. If the average FRAGMENT size is 250bp. How should I set the insertion size: Should it be 250-150=100bp OR 250 - 150*2 = -50 OR set it as 0...
03 March 2015 2,867 3 View
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...
03 March 2015 5,882 3 View
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...
02 February 2015 5,875 2 View
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...
10 October 2013 4,353 4 View
Has anyone ever used Phusion for BS-PCR? could you give me the PCR profile? our lab is running out of HotStar Taq, but has sufficient Phusion, so I am trying to use Phusion to do my BS-PCR, and it...
03 March 2013 10,127 0 View
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...
02 February 2013 7,974 0 View
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...
01 January 2013 3,637 6 View
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...
09 September 2012 3,562 0 View
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...
08 August 2012 5,460 4 View
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...
07 July 2012 9,589 7 View
