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Forum: Bioinformatics 08-10-2016, 02:45 AM
Replies: 3
Views: 2,431
Posted By Jluis
Dear kmcarr, Thank you very much for your...

Dear kmcarr,

Thank you very much for your answer!
I'm currently on holidays, but I will try to test your solution as soon as I get back to work.

Best

JL
Forum: Bioinformatics 08-05-2016, 02:41 AM
Replies: 3
Views: 2,431
Posted By Jluis
Issue with FASTA header in QIIME

Dear all,

I have to analyze a set of 26 samples of 16S amplicon data, coming from 250 nt Paired-end Illumina Hi-Seq reads. When I received those sequences they were already demultiplexed , merged...
Forum: Bioinformatics 09-30-2014, 07:20 AM
Replies: 0
Views: 1,019
Posted By Jluis
miRNA gene promoter analysis

Dear all,

Does anybody know about a webtool, local tool or R-package able to analyze miRNA promoters using a list of miRNA ids as input?

Any other alternative approach (e.g. not using the id...
Forum: Bioinformatics 04-09-2013, 11:11 PM
Replies: 2
Views: 1,069
Posted By Jluis
Thank you very much for your answer pm 2012. ...

Thank you very much for your answer pm 2012.
The tools you suggested look very nice and fit perfectly to our requirements.

With best wishes

JL
Forum: Bioinformatics 04-08-2013, 06:16 AM
Replies: 2
Views: 1,069
Posted By Jluis
Any tool for SNP functionality prediction?

Hello everybody,

Does anybody known about a tool that predicts SNP functionality using a list of SNP as input? If possible, I'd need a command line tool or if it's an online tool I'd need to be...
Forum: Bioinformatics 04-08-2013, 04:57 AM
Replies: 2
Views: 2,274
Posted By Jluis
Hi slny, Have a look at this pipeline. It...

Hi slny,

Have a look at this pipeline. It has been set up by the ENCODE project as a reference for ChIPseq analysis.

https://sites.google.com/site/anshulkundaje/projects/idr

By the way, I'd...
Forum: Bioinformatics 02-05-2013, 02:12 AM
Replies: 5
Views: 1,634
Posted By Jluis
@swbarnes2 I've followed your instructions...

@swbarnes2

I've followed your instructions and then included another couple of steps to perform the whole (to my lack of experience with this particular analysis) study.

Do you consider this a...
Forum: Bioinformatics 01-31-2013, 12:47 AM
Replies: 5
Views: 1,634
Posted By Jluis
Dear swbarnes2, You're right in everything,...

Dear swbarnes2,

You're right in everything, the program I need is intersectBed. I got it wrong because I didn't understand its functions from the online instructions I referred to yesterday. I've...
Forum: Bioinformatics 01-30-2013, 06:18 AM
Replies: 5
Views: 1,634
Posted By Jluis
@ swbarnes2, thank you very much for your kind...

@ swbarnes2, thank you very much for your kind help.
I'd like to ask you a question about bedtools if I may. I've been reading the description of the different bed-tools...
Forum: Bioinformatics 01-29-2013, 02:18 AM
Replies: 5
Views: 1,634
Posted By Jluis
Resequencing & variant calling issue

Dear all,

I have to analyze a set of samples that come from a re-sequencing project.
I've been given the coordinates where the genes under analysis (those I should carry out a variant calling...
Forum: Bioinformatics 01-06-2013, 11:28 PM
Replies: 2
Views: 2,747
Posted By Jluis
Thank you frozenlyse, I'll take a look at it and...

Thank you frozenlyse, I'll take a look at it and see if it works in my particular analysis.

;)
Forum: Bioinformatics 01-04-2013, 03:30 AM
Replies: 2
Views: 2,747
Posted By Jluis
How to classify promoters according to CpG density

Hello everybody,

A research collaborator has asked us to classify promoters according to their CpG density. Data comes from a RRBS (Reduced Representation Bisulfite Sequencing) analysis in mouse...
Forum: Bioinformatics 01-04-2013, 02:41 AM
Replies: 1
Views: 3,081
Posted By Jluis
Hello Turnersd, Did you figure out a way to...

Hello Turnersd,

Did you figure out a way to calculate and plot the methylation density?

I'll appreciate if you could give me any insight on how to do this.

Thanks in advance
Forum: Bioinformatics 01-01-2013, 11:29 PM
Replies: 2
Views: 1,545
Posted By Jluis
@caballien I had to clean my reference file...

@caballien

I had to clean my reference file (.gtf) getting rid of any "chrM" or "_random" line. To achieve this I used a very simple Perl script (I'm sure there are faster ways to do it using...
Forum: Bioinformatics 12-14-2012, 02:46 AM
Replies: 6
Views: 4,777
Posted By Jluis
@paolo.kunder thank you for this insight I was...

@paolo.kunder thank you for this insight I was trying to use GSEA for enrichment analysis instead of TF searches. It seems to work quite nicely ;)
Forum: Bioinformatics 12-14-2012, 02:22 AM
Replies: 6
Views: 4,777
Posted By Jluis
Thank you everybody for your insights ...

Thank you everybody for your insights

@bruce01 and @zinky, IPA and TRansfac are commercial as you point out and I don't have the budget to purchase them...

@bruce I agree with you in the RNAseq...
Forum: Bioinformatics 12-13-2012, 12:01 AM
Replies: 6
Views: 4,777
Posted By Jluis
Is there a way to get transcription factors from gene list?

Hello everybody,

During a RNA-seq experiment analysis I've receiver the request of getting the Transcription factors (TF) associated to the names of the Differentially expressed (DE) genes. I've...
Forum: Bioinformatics 11-13-2012, 05:53 AM
Replies: 15
Views: 2,591
Posted By Jluis
Hello again, I'll try to answer your...

Hello again,

I'll try to answer your questions again:

-What was the exact problem when you could not "demultiplex" this data the first time around?

We don't know, it just didn't work, maybe...
Forum: Bioinformatics 11-13-2012, 04:43 AM
Replies: 15
Views: 2,591
Posted By Jluis
Hello again, @GenoMax, I'll answer your...

Hello again,

@GenoMax, I'll answer your questions as accurately as I can ;)

-The only set of files you currently have were analyzed by providing no index info for lane 3?

Yes, te only set...
Forum: Bioinformatics 11-13-2012, 12:34 AM
Replies: 15
Views: 2,591
Posted By Jluis
Dear GenoMax, I have no files from the old...

Dear GenoMax,

I have no files from the old analysis, and after trying your code on the "undemultiplexed" Lane3 fastq file, it seems no index info is present in the reads, since the scripts results...
Forum: Bioinformatics 11-09-2012, 04:11 AM
Replies: 15
Views: 2,591
Posted By Jluis
Thank you GenoMax, but after running the...

Thank you GenoMax, but after running the samplesheet with no index the info from the Undetermined doesn't give me any clue, although we have the spike in fastq there (as it should)...
Forum: Bioinformatics 11-09-2012, 03:57 AM
Replies: 15
Views: 2,591
Posted By Jluis
After demultiplexing without the barcode...

After demultiplexing without the barcode (following C.R. advice), we have retrieved a Fastq file. In this file we expect to have the reads of the 2 samples and also the reads of the Phi-X we used as...
Forum: Bioinformatics 11-09-2012, 02:11 AM
Replies: 15
Views: 2,591
Posted By Jluis
Thank you for your answers C.R. and kmcarr ...

Thank you for your answers C.R. and kmcarr

I'll try the C.R. strategy and see what happens. I'll cross fingers and see if any data can be rescued for further processing...
Forum: Bioinformatics 11-08-2012, 06:31 AM
Replies: 15
Views: 2,591
Posted By Jluis
Yes, the samplesheet is correct, samples and...

Yes, the samplesheet is correct, samples and barcodes are specified exactly the same way as they are for the other lanes. We've tried multiple "solutions" the Illumina tech-support offered us but...
Forum: Bioinformatics 11-08-2012, 12:04 AM
Replies: 15
Views: 2,591
Posted By Jluis
Illumina HiScanSQ not decoding 1 Lane

Dear all,

We have experienced a weird issue with our last sequencing run in a Illumina HiScanSQ with a flowcell where samples were multiplexed.
Every lane of the flowcell unless Lane3 have been...
Showing results 1 to 25 of 44

 


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