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Forum: Bioinformatics 02-11-2015, 11:02 AM
Replies: 27
Views: 19,032
Posted By raphael123
A possible problem : According to htseq...

A possible problem :

According to htseq documentation : http://www-huber.embl.de/users/anders/HTSeq/doc/counting.html

"The fact that the records describe the same fragment can be seen from the...
Forum: Bioinformatics 11-10-2014, 04:22 PM
Replies: 13
Views: 7,538
Posted By raphael123
Hi Michael, Thanks for all this details in...

Hi Michael,

Thanks for all this details in these thread, I have a simple first question :
Is it possible to simply remove those outliers from the analysis ? I have a 25 vs 25 case control study,...
Forum: Bioinformatics 11-03-2014, 01:44 PM
Replies: 123
Views: 48,820
Posted By raphael123
Hi ! I update my DEseq2 package to 1.4.5....

Hi !

I update my DEseq2 package to 1.4.5. Now my replaceOutliersWithTrimmedMean function is not replacing anything ! I have a very clear outlier that was remove previously and now any way I call...
Forum: Epigenetics 10-22-2014, 10:37 AM
Replies: 53
Views: 8,169
Posted By raphael123
Ok I don t know about BSmooth aligner ... ...

Ok I don t know about BSmooth aligner ...

What we do is :
trimming + quality filter
bismark using bowtie2
BisSNP to improve alignment and call methylation
meth diff using bssmooth( we are...
Forum: Epigenetics 10-22-2014, 10:00 AM
Replies: 53
Views: 8,169
Posted By raphael123
Okay, I am surprise bowtie2 can call methylation...

Okay, I am surprise bowtie2 can call methylation ... I would advise you to use BisSNP to call your methylation from aligned file, then you will still have the strand information and can format it to...
Forum: Epigenetics 10-22-2014, 08:58 AM
Replies: 53
Views: 8,169
Posted By raphael123
First you should get the strand information for...

First you should get the strand information for each position !
Could you show the first lines of your bed file ?
Forum: Epigenetics 10-22-2014, 08:56 AM
Replies: 0
Views: 1,390
Posted By raphael123
piwi RNA / good practices

Hi ! I had hard time finding a good piwi database so here is what I did, you can use it and tell me if it seems reasonable.
http://pirnabank.ibab.ac.in is the most used database, thez give you a...
Forum: Bioinformatics 08-26-2014, 05:04 PM
Replies: 1
Views: 2,245
Posted By raphael123
I have troubles using miRDeep2 too, you should...

I have troubles using miRDeep2 too, you should realign using your new genome.
because I guess reads_collapsed.fa was built before...
So bowtie-build on ssa.merged.genome.fa then mapper.pl etc ...
Forum: Bioinformatics 07-21-2014, 02:21 PM
Replies: 8
Views: 8,119
Posted By raphael123
Thanks Mickael, I found the way to use continuous...

Thanks Mickael, I found the way to use continuous covariate, it was simple !
Now to test the change relative for each patient, I should fit a GLM including the subject identifier, i.e. "~ patient +...
Forum: General 07-21-2014, 02:10 PM
Replies: 2
Views: 3,542
Posted By raphael123
Hi Simon ! Usually each coeficient in a GLM is...

Hi Simon !
Usually each coeficient in a GLM is associated with a p value, do you know how to get these p value from the GLM of DEseq ?
Forum: Bioinformatics 07-17-2014, 10:03 AM
Replies: 8
Views: 8,119
Posted By raphael123
Thanks Ecolliso, I would say that you have...

Thanks Ecolliso,

I would say that you have the same kind of design that I have, maybe more complex. I am trying to understand what I can do in DESeq1 or 2

I can answer to

adjustment on p...
Forum: Bioinformatics 07-16-2014, 03:54 PM
Replies: 8
Views: 8,119
Posted By raphael123
Reading that and the DESeq vignette I am still...

Reading that and the DESeq vignette I am still confuse :



Here the p value for a single row (in this case let s say RNA) is testing a null hypothesis.
I can t formulate it, is it the...
Forum: Bioinformatics 07-02-2014, 01:33 PM
Replies: 6
Views: 6,779
Posted By raphael123
Hi, I am confronting the same problem, in silico...

Hi, I am confronting the same problem, in silico digestion for CCGG .
I have a file with hg19 and one line per chromosome sequence and I do :


cat hg19.txt | sed "s/CCGG/\n/g" | awk...
Forum: Bioinformatics 06-30-2014, 12:23 PM
Replies: 16
Views: 7,923
Posted By raphael123
Oh ! so featureCounts is a tool to construct a...

Oh ! so featureCounts is a tool to construct a count table from a sam/bam file ?
Thank you !
Forum: Bioinformatics 06-30-2014, 12:00 PM
Replies: 16
Views: 7,923
Posted By raphael123
Thanks for your answer !| So there is no way to...

Thanks for your answer !|
So there is no way to get the read counts from cuff-tools ? Maybe I miss something here..
Forum: Bioinformatics 06-30-2014, 11:39 AM
Replies: 16
Views: 7,923
Posted By raphael123
No the raw count table: I would like...

No the raw count table:



I would like to analyse the raw count with DESeq2
Forum: Bioinformatics 06-30-2014, 10:08 AM
Replies: 16
Views: 7,923
Posted By raphael123
Do you think there is a way to get the raw count...

Do you think there is a way to get the raw count in a readable format for DESeq ?
Or a way to read the binary file ? I can t find that !
Forum: Bioinformatics 04-23-2014, 10:06 AM
Replies: 4
Views: 1,914
Posted By raphael123
I guess you talk about pair end sequencing, we...

I guess you talk about pair end sequencing, we are talking about a atrand bias, a difference of methylation between FORWARD and REVERSE strand ...
Forum: Bioinformatics 04-22-2014, 12:48 PM
Replies: 4
Views: 1,914
Posted By raphael123
I like this question ... And I am interested !

I like this question ... And I am interested !
Forum: Bioinformatics 03-31-2014, 07:42 AM
Replies: 57
Views: 34,612
Posted By raphael123
Hi everybody, to help your discussion I can just...

Hi everybody, to help your discussion I can just give as an advice to NOT USE fastx_toolkit for pair end library.
According to the authors, this tool was done for SHORT MOLECULE only. (e.g. shorter...
Forum: Bioinformatics 02-18-2014, 08:18 AM
Replies: 4
Views: 5,616
Posted By raphael123
Thank you ! We have the same output ! Your code...

Thank you ! We have the same output ! Your code is more elegant but harder to understand :)
equivalent of :

p.adjust(pval,method="BH")
Forum: Bioinformatics 02-17-2014, 12:24 PM
Replies: 4
Views: 5,616
Posted By raphael123
Benjamini–Hochberg procedure in R

Tell me if I am wrong but this is the Benjamini–Hochberg procedure is that simple ?


# produce a table of FDR using with pval already sorted in increasing order
fdr = function(pval){

...
Forum: Bioinformatics 02-07-2014, 05:07 PM
Replies: 14
Views: 26,174
Posted By raphael123
Very usefull discussion ! Syfo you are rigth...

Very usefull discussion !

Syfo you are rigth but it is not explaining this difference :



knchess don t you think it depend how much you try to scan the full genome ? Is the first locus...
Forum: Bioinformatics 01-30-2014, 09:07 AM
Replies: 2
Views: 4,992
Posted By raphael123
In my case, a pair of read align slearly both on...

In my case, a pair of read align slearly both on chromosome 3 on end to end.
By setting local I have the pair split between 2 chromosmes, I have a better match at a wrong place ..
I feel like I don...
Forum: RNA Sequencing 01-28-2014, 09:51 AM
Replies: 2
Views: 2,182
Posted By raphael123
1. To normalise sample 1 THEN sample 2 is...

1. To normalise sample 1 THEN sample 2 is equivalent as normalizing sample 1 PLUS sample 2 .. AS long as you accept to normalize with the DESeq way.

2. Some experiment have no hit .. You can t...
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