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Forum: Bioinformatics 01-31-2017, 09:07 AM
Replies: 13
Views: 6,542
Posted By sbcn
Hi, I think this should work: ...

Hi,

I think this should work:

biomart="plants_mart"
host="plants.ensembl.org"
biomaRt_dataset ="athaliana_eg_gene"
goAnno ="org.At.tair.db"

source:...
Forum: Bioinformatics 01-31-2017, 08:58 AM
Replies: 0
Views: 1,029
Posted By sbcn
RIPSeeker "Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) : .

Hi all,

I am using ripSeek function from RIPSeeker package (on a RIP-seq data set), the following way:

seekOut <- ripSeek(bamPath=mybamfiles,
cNAME="EXP",
strandType="-",...
Forum: Bioinformatics 12-20-2016, 05:19 AM
Replies: 4
Views: 1,828
Posted By sbcn
Thank you both for your replies. So it there a...

Thank you both for your replies.
So it there a way that I can convert or reduce the data from genes to compounds? I am not very familiar with this...
Forum: Bioinformatics 12-15-2016, 02:14 AM
Replies: 4
Views: 1,828
Posted By sbcn
pathview failing on metabolic pathways

Dear all,

I am using R package "pathview" to map my data to B.cereus (bce) KEGG networks.

It works very well with most networks, but I can make it work with the metabolic pathways, for example,...
Forum: Bioinformatics 02-17-2016, 01:48 AM
Replies: 6
Views: 6,824
Posted By sbcn
Thanks a lot for your input. I have now...

Thanks a lot for your input.

I have now tried gffcompare, but it is actually a lot worse in my case:

gffcompare -r reference.gtf -s reference.fa -C -D -i gtf_list.txt

awk '$3=="transcript"'...
Forum: Bioinformatics 02-15-2016, 03:05 AM
Replies: 6
Views: 6,824
Posted By sbcn
stringtie parameters

Hi,

I have been trying to use Stringtie for transcriptome re-assembly, based on a reference gtf file.
Here is how I ran it:

# for each of the bam files from my project (aligned with tophat2):...
Forum: Bioinformatics 11-19-2015, 01:18 AM
Replies: 1
Views: 1,045
Posted By sbcn
Anyone?

Hi, does someone have an opinion or some tip about this?
Thanks!
Forum: Bioinformatics 11-16-2015, 08:04 AM
Replies: 1
Views: 1,045
Posted By sbcn
DESeq2 LRT / 2-way ANOVA?

Dear all,

Let's start from the experiment (RNA-seq) I would like to analyse:
3 time points (t0, t1, t3)
2 different parts of the brain (front, back)
2 different layers of the brain - say...
Forum: Bioinformatics 09-14-2015, 12:38 AM
Replies: 5
Views: 3,043
Posted By sbcn
Thanks Devon! I don't think your explanation is...

Thanks Devon!
I don't think your explanation is unclear, it is just the whole concept that is quite hard to understand...

Given your last answer: does it mean that my model is wrong, in the sense...
Forum: Bioinformatics 09-10-2015, 04:47 AM
Replies: 5
Views: 3,043
Posted By sbcn
Hi Devon, Thanks a lot for your answer! ...

Hi Devon,

Thanks a lot for your answer!

There is something unclear to me regarding this, and regarding what I had previously posted.
There are several "1s" present in the pairs information, so...
Forum: Bioinformatics 09-09-2015, 03:17 AM
Replies: 5
Views: 3,043
Posted By sbcn
DESeq2 paired data: "model is not full rank"

Dear all,

I have a question that is similar to others I've seen, but I am still not sure how to solve it.

Data is:
* RNA-seq from Illumina Hiseq machine
* Mus musculus
* 24 samples

Input...
Forum: Bioinformatics 07-22-2015, 02:39 AM
Replies: 0
Views: 1,377
Posted By sbcn
ChIP-seq annotation bidirectional promoters: any tool?

Hi all,

I am annotating peaks from a ChIP-seq experiment.

The problem I face is that some of the peaks fall on bidirectional promoters.

I would like to be able to get an output annotation...
Forum: Bioinformatics 10-30-2014, 02:38 AM
Replies: 46
Views: 15,431
Posted By sbcn
I have finally completely uninstalled and...

I have finally completely uninstalled and re-installed RSQLite as suggested, and it solved the problem!
Although it was loaded in the session previously and it is the same version of the package,...
Forum: Bioinformatics 10-29-2014, 06:57 AM
Replies: 46
Views: 15,431
Posted By sbcn
Same problem here, just updated to the latest...

Same problem here, just updated to the latest version cummeRbund (cummeRbund_2.8.0) and I get an error I didn't get some weeks ago when I last used cuffdiff+cummeRbund:

cuff<-readCufflinks()...
Forum: Bioinformatics 10-17-2012, 07:33 AM
Replies: 3
Views: 2,413
Posted By sbcn
Any idea anyone?

Any idea anyone?
Forum: Bioinformatics 10-16-2012, 01:29 AM
Replies: 3
Views: 2,413
Posted By sbcn
Bowtie 2 multiple alignment default mode: how the best one is chosen?

Dear all,

I am using Bowtie 2 and I have a question about multiple alignments: I am using the default mode which, according to the documentation "search for multiple alignments, report the best...
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