Mohamed Belhocine

14 Questions 25 Answers 0 Followers

Questions related from Mohamed Belhocine

What is the best way to make an in-house database with allele frequency ?

Hi, I am currently working on making a variants database. I generate seperate VCF files for each samples them and merge them using VCFtools (using mergeVCF command) to make a multisample VCF...

01 January 2018 8,278 6 View

Sambamba-sort problem (not enough data in stream) ?

Hello, I'm getting an error: "sambamba-view: not enough data in stream" by running sambamba-sort, below my script : PS: I get this error only for some bam files but for all !! "sambamba view -t...

02 February 2017 5,091 0 View

How to create a test predictor with the genotype case/control study (genetic association) ?

Hello,I have a Case / Control genotype study (one qualitative phenotype). so I carried a genetic association analysis with PLINK (logistic) and I've identified hundreds of SNPs with very low Pval...

08 August 2016 1,476 4 View

How to calculate Gene-Gene Pearson correlation ?

I am stuck with a very simple problem. I want to build a Pearson correlation matrix for my RNA-seq dataset. My data file consists of normalized, log-transformed expression values of 60k...

01 January 2016 7,145 13 View

What option do you usually use with featureCounts to have count according to isoform ?

I am somewhat new to RNAseq data and I have been using featureCounts from the subread package to summarize reads/fragments across genomic features (genes, transcripts). In particular I am...

10 October 2015 5,088 1 View

How can I make a Polytomous analysis to define clusters in RNA-seq count data?

Hello, I have a RNA-seq count Data, with several conditions. and I'd like to do to a polytomous analysis to find the different clusters and their respective gene signatures. I find le package in R...

04 April 2015 5,413 3 View

How can I do clustering with RNA-Seq data ?

I have Cuffdiff (--no-diff) output tables and I want to perform clustering : 1) better to use Count or FPKM ? 2) Are "standard" clustering algorithms appropriate for RNA-Seq data due to its...

03 March 2015 7,733 23 View

How can I calculate the average values in dataframe with R?

I have a dataframe with a first column contains the gene symbol and the others column contains an expression values. the Column of symbol can contain the same symbol more then one time. So I would...

03 March 2015 2,073 5 View

Does anyone know how to estimate the inflection point using r?

How can I get the inflection point using r ?

02 February 2015 6,548 5 View

Is there a tool for converting a variable step wig to a fixed step wig?

Is there a tool for converting a variable step wig to a fixed step wig? Thank you in advance for your help

02 February 2015 986 5 View

How can one convert a nucleotide-space to a color-space format ?

Does anybody know where I could find a tool to convert a nucleotide-space sequence to a color-space sequence? Thanks a lot in advance,

11 November 2014 4,124 5 View

How to convert FASTQ to csFASTA and QUAL ?

After using cutadapt where I gave as input the pair csfasta and qual, I got FASTQ like a output file. But,I need csfasta file and qual. There are a tool to do that ?

10 October 2014 3,306 2 View

Why is there a missing transcripts in the output file (isoforms.fpkm_tracking)?

When I launch cufflink with the -g option, the output file does not contain all the transcripts provided in the GTF annotation file. And it is no the same missing transcripts in the output file...

10 October 2014 4,964 3 View

Can anyone suggest me the best way to normalize the RNA-seq data ?

Could someone tell me the best way of normalizing RNA-seq data in order to make a comparison between several samples ?

09 September 2014 3,839 3 View