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Forum: RNA Sequencing 05-21-2019, 01:24 AM
Replies: 0
Views: 1,030
Posted By NicoBxl
RNA-Seq on FFPE samples : Illumina TruSeq RNA exome or Roch Kapa HMR kit

Hi,

I've ~300 FFPE samples to analyzed using RNA-Seq. I've two possibilities for the library prep depending on the sequencing center I will chose.

Either :

Illumina TruSeq RNA Exome :...
Forum: Bioinformatics 04-10-2014, 05:49 AM
Replies: 6
Views: 1,211
Posted By NicoBxl
read DESeq paper :...

read DESeq paper : http://genomebiology.com/2010/11/10/R106 and also DESeq vignette that is pretty well done.
or maybe edgeR paper also
Forum: Bioinformatics 04-10-2014, 05:41 AM
Replies: 6
Views: 1,211
Posted By NicoBxl
why do you use a ttest and not DESeq test (based...

why do you use a ttest and not DESeq test (based on negative binomial) ? RNA-Seq data do not follow a normal distribution.

for normalized count, you can use also : normalizedCounts <-...
Forum: Bioinformatics 04-10-2014, 05:35 AM
Replies: 6
Views: 1,211
Posted By NicoBxl
use DESeq or edgeR ( in R ) to normalize and...

use DESeq or edgeR ( in R ) to normalize and check for DE genes
Forum: Illumina/Solexa 04-03-2014, 04:06 AM
Replies: 58
Views: 45,829
Posted By NicoBxl
if it's single-end, you don't have to precise the...

if it's single-end, you don't have to precise the type of library.
Forum: Bioinformatics 03-31-2014, 06:11 AM
Replies: 12
Views: 4,047
Posted By NicoBxl
like dpryan said, if you are time limited, use...

like dpryan said, if you are time limited, use STAR ( very very fast and same, even better results than tophat
Forum: RNA Sequencing 02-18-2014, 10:40 PM
Replies: 4
Views: 5,651
Posted By NicoBxl
Hi guys, I did 2x100 finally, and it worked...

Hi guys,

I did 2x100 finally, and it worked pretty well ;)
Forum: Bioinformatics 02-10-2014, 01:26 AM
Replies: 6
Views: 3,248
Posted By NicoBxl
you could use DESeq. There is a no-replicate...

you could use DESeq. There is a no-replicate mode.

And of course confirm the expression of several candidates by other methods like qRT-PCR
Forum: Bioinformatics 02-10-2014, 12:37 AM
Replies: 6
Views: 3,248
Posted By NicoBxl
Be very carefull not to make assomption on your...

Be very carefull not to make assomption on your results and to force your data to output something. That's not how science works.
Forum: Bioinformatics 02-07-2014, 01:02 AM
Replies: 6
Views: 3,470
Posted By NicoBxl
or just use STAR that do not need to specify...

or just use STAR that do not need to specify inner distance. and also is much faster for the same ( even better ) results
Forum: RNA Sequencing 11-14-2013, 05:07 AM
Replies: 5
Views: 1,622
Posted By NicoBxl
Could you post a picture of your alignment.

Could you post a picture of your alignment.
Forum: RNA Sequencing 09-25-2013, 01:22 AM
Replies: 4
Views: 5,193
Posted By NicoBxl
I don't think it's a good idea. It's always...

I don't think it's a good idea. It's always better to map to all the transcript because your data is coming from total RNA ( or poly-A RNA). It can happen that when you map to your subset, some...
Forum: Bioinformatics 08-27-2013, 01:39 AM
Replies: 2
Views: 2,057
Posted By NicoBxl
And is it a good idea to perform expression...

And is it a good idea to perform expression analysis using both unstranded and stranded samples ? using htseq-count and DESeq for example ?
Forum: Bioinformatics 08-22-2013, 11:35 PM
Replies: 9
Views: 10,395
Posted By NicoBxl
DESeq2 error : the model matrix is not full rank

Hi,

I've got an error in a DESeq2 analysis. So I've 30 samples, with a 3 factor design. So I put a Replicate column in my design . it's for technical replicate. I don't know if it's a good idea......
Forum: RNA Sequencing 08-22-2013, 04:01 AM
Replies: 0
Views: 1,490
Posted By NicoBxl
Biological and technical replicates in expression analysis (DESeq)

Hi,

I've to analyze several RNA-Seq samples. I've samples from several runs, unstraned and straned, and several samples sequenced multiple times ( using different library kit ). I used htseq-count...
Forum: Illumina/Solexa 07-01-2013, 04:38 AM
Replies: 2
Views: 1,899
Posted By NicoBxl
Illumina stranded RNA-Seq background problem

Hi everybody,

We perform RNA-Seq experiments using illumina TruSeq total RNA stranded (with RiboZero) and we have strange results compared to previous samples. We sequenced on a HiSeq2000 2x100bp....
Forum: RNA Sequencing 06-06-2013, 11:42 PM
Replies: 35
Views: 22,783
Posted By NicoBxl
Yes that seems interesting to analyze. 1500 extra...

Yes that seems interesting to analyze. 1500 extra DE genes seems a lot.. I suppose you used the same count matrix as input ?
Forum: RNA Sequencing 05-22-2013, 05:46 AM
Replies: 3
Views: 1,193
Posted By NicoBxl
It's pretty strange to find miRNAs because there...

It's pretty strange to find miRNAs because there are not polyA in their mature state (only poly-A in the pri-miRNA state)
Forum: RNA Sequencing 04-16-2013, 01:51 AM
Replies: 11
Views: 9,675
Posted By NicoBxl
no use the power of piping ;) gzip -d -c...

no use the power of piping ;)

gzip -d -c input.fastq.gz | wc -l
Forum: Illumina/Solexa 04-15-2013, 02:46 AM
Replies: 9
Views: 3,867
Posted By NicoBxl
Unfortunately all big computing grid work on a...

Unfortunately all big computing grid work on a unix-based system..and so this tool is born dead...
Forum: RNA Sequencing 04-15-2013, 01:17 AM
Replies: 4
Views: 2,537
Posted By NicoBxl
use intersectbed from bedtools...

use intersectbed from bedtools https://code.google.com/p/bedtools/
Forum: Bioinformatics 04-12-2013, 01:13 AM
Replies: 7
Views: 1,111
Posted By NicoBxl
yes, check the IGV manual to have more infos :...

yes, check the IGV manual to have more infos : http://www.broadinstitute.org/igv/
Forum: Bioinformatics 04-12-2013, 12:42 AM
Replies: 7
Views: 1,111
Posted By NicoBxl
you should convert your blast output to gff....

you should convert your blast output to gff. Check here http://www.biostars.org/p/277/
Forum: Bioinformatics 04-12-2013, 12:28 AM
Replies: 7
Views: 1,111
Posted By NicoBxl
IGV has several genomes in its database, but it...

IGV has several genomes in its database, but it accept also fasta files.
Forum: Bioinformatics 04-12-2013, 12:16 AM
Replies: 7
Views: 1,111
Posted By NicoBxl
I you have a bam file from an aligner (you used...

I you have a bam file from an aligner (you used bowtie, but you should use a splice-aware aligner like tophat or STAR) and a gtf (or gff) from cufflinks, you can use IGV to visualize the alignment...
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