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Forum: Bioinformatics 05-31-2016, 08:39 AM
Replies: 5
Views: 2,243
Posted By bernardo_bello
What does 'rU' refers to? a second input file?

What does 'rU' refers to? a second input file?
Forum: Illumina/Solexa 03-25-2016, 10:49 AM
Replies: 1
Views: 1,296
Posted By bernardo_bello
Question Bias due to DNA extraction kit and illumine version used

Do you think DNA extraction kit and illumine version used could be a source of variation?
Our idea is to perform genome comparison with bacterial genomes whose DNA was extracted using different DNA...
Forum: Literature Watch 09-22-2014, 01:19 AM
Replies: 1
Views: 2,548
Posted By bernardo_bello
You may check these papers yourself, maybe they...

You may check these papers yourself, maybe they sequenced this kind of samples:

("Metagenomics"[Mesh]) AND "Mouth"[Mesh]

I think hmp consortia have already sequenced from mouth, check their...
Forum: Bioinformatics 06-19-2014, 04:08 AM
Replies: 4
Views: 3,256
Posted By bernardo_bello
In my case: R2 is the forward R1 is the...

In my case:

R2 is the forward
R1 is the reverse
Forum: Bioinformatics 06-03-2014, 11:09 PM
Replies: 14
Views: 7,784
Posted By bernardo_bello
Thanks, seems there is not an associated...

Thanks, seems there is not an associated publication for SMALT. There is?
Forum: RNA Sequencing 05-12-2014, 05:26 AM
Replies: 2
Views: 1,620
Posted By bernardo_bello
Thanks for the feedback. Bernardo

Thanks for the feedback.
Bernardo
Forum: RNA Sequencing 05-11-2014, 02:42 AM
Replies: 2
Views: 1,620
Posted By bernardo_bello
Post Is this edgeR code OK?

Hi,

I would you to revise my edgeR code since it's possible I missed something important because being quite new on this.

Thanks, Bernardo

P.S. This questions has also been posted in Biostar...
Forum: Bioinformatics 04-16-2014, 03:36 AM
Replies: 0
Views: 1,353
Posted By bernardo_bello
Cool Best strategy to get GO terms for a proteome?

Hi,

I would like to know the best strategy to get the highest amount of GO terms for the bacterial proteome I'm working. Since it's a non-model organism, I will build the GO database from scratch....
Forum: RNA Sequencing 04-03-2014, 04:35 AM
Replies: 3
Views: 1,604
Posted By bernardo_bello
Could you share you commands? Thanks!

Could you share you commands? Thanks!
Forum: Bioinformatics 04-03-2014, 02:01 AM
Replies: 2
Views: 1,441
Posted By bernardo_bello
Close bacterial draft genome with other draft genome

Hi,

I would like to reduce contig number of the bacterial draft genome I'm trying to close. The draft genome is in 47 contigs and has been assembled by me, using Phred, Phrap, Consed.

I'm...
Forum: RNA Sequencing 04-02-2014, 01:12 AM
Replies: 3
Views: 1,604
Posted By bernardo_bello
Looking for tools to find non-coding RNAs in bacterial RNA-seq data

Hi,

I'm looking for tools to semi-automate finding non-coding RNAs in bacterial RNA-seq data. I've been able to find these...
Forum: Literature Watch 12-18-2013, 08:09 AM
Replies: 4
Views: 4,054
Posted By bernardo_bello
I tried L_RNA_scaffolder and got nice result...

I tried L_RNA_scaffolder and got nice result (reduced contig number) although manual check was not performed.
Forum: RNA Sequencing 12-04-2013, 10:40 AM
Replies: 0
Views: 1,680
Posted By bernardo_bello
Post RT-qPCR: which dilutions in calibration curve?

I've seen in MIQE guidelines that calibration curves a needed when performing RT-qPCR. I'll use genomic DNA to perform these calibration curves.

My question is that I don't know the range of...
Forum: Bioinformatics 11-30-2013, 09:05 AM
Replies: 0
Views: 1,589
Posted By bernardo_bello
Post How to get conservation of vaccine candidates between hundreds of bacterial strains?

Hi community,

We have identified vaccine candidates via an ex-vivo RNA-seq approach. Next step would be to perform conservation of these candidates (about 20) between multiple bacterial strains...
Forum: RNA Sequencing 11-22-2013, 01:23 AM
Replies: 7
Views: 6,352
Posted By bernardo_bello
Cool Mine is: -mapping with TMAP (Ion Torrent...

Mine is:

-mapping with TMAP (Ion Torrent specific)
-counting with HTSeq
-edgeR for differential expression
-TopGO for enrichment, previously run Blast2GO if working with non-model organism.
...
Forum: Literature Watch 10-28-2013, 02:32 AM
Replies: 4
Views: 4,054
Posted By bernardo_bello
Smile Hi there, I have been using a bacterial...

Hi there,

I have been using a bacterial draft genome from GenBank for RNA-seq
project. In order to reduce genome contig number, I used L_RNA_scaffolder
tool, so I had to reannotate again this...
Forum: RNA Sequencing 10-21-2013, 02:26 AM
Replies: 0
Views: 1,924
Posted By bernardo_bello
Smile Too many DEG with edgeR output?

Hi there,

I'm dealing with bacterial RNA-seq analysis. My experiment is very simple. Two samples to compare and no replicates. Reads were generated with Ion Torrent PGM using 316 chip. One for...
Forum: RNA Sequencing 10-18-2013, 02:46 AM
Replies: 1
Views: 1,498
Posted By bernardo_bello
https://docs.google.com/file/d/0B8-ZAuZe8jldNUNhZk...

https://docs.google.com/file/d/0B8-ZAuZe8jldNUNhZkdVbV9YQXM/edit?usp=sharing
Forum: RNA Sequencing 10-18-2013, 02:44 AM
Replies: 1
Views: 1,498
Posted By bernardo_bello
Smile Is this a valid GFF3 file for HTSeq?

Hi there,

I created a gff3 file from GenBank file containing multiple contigs (using Bioperl 'genbank2gff3.pl' tool) . In order to run HTSeq I removed the ##FASTA section (HTSeq doesn't likes). My...
Forum: RNA Sequencing 10-09-2013, 02:30 AM
Replies: 0
Views: 1,612
Posted By bernardo_bello
Smile NCBI standards for genome annotation after contig reduction

Hi community,

I have been using a bacterial draft genome from GenBank for RNA-seq project. In order to reduce genome contig number, I used L_RNA_scaffolder...
Forum: RNA Sequencing 05-14-2013, 11:25 AM
Replies: 0
Views: 1,044
Posted By bernardo_bello
Post Does dPCR fits RNA-seq validation?

Hi community,

I'm was looking for qPCR standards to start differential RNA-seq results validation and I found digital PCR (dPCR) technique.

First, I would like to know if it's good idea to use...
Forum: RNA Sequencing 05-08-2013, 11:22 AM
Replies: 1
Views: 3,244
Posted By bernardo_bello
Smile Hi Dolphin22, I will analyse an sRNA sample...

Hi Dolphin22,

I will analyse an sRNA sample soon. I thought using this tool to start.

It will be useful to post here our satisfaction with this new tool.

Regards,

Bernardo
Forum: RNA Sequencing 05-08-2013, 08:56 AM
Replies: 2
Views: 1,372
Posted By bernardo_bello
I'm also in search of bacterial qPCR standards. ...

I'm also in search of bacterial qPCR standards.

Bernardo
Forum: Bioinformatics 04-21-2013, 06:03 AM
Replies: 15
Views: 12,000
Posted By bernardo_bello
SOLVED! Copy corrupted .sam file Rename...

SOLVED!

Copy corrupted .sam file

Rename copied corrupted .sam file

Run samtools view

Now worked for me!
Forum: Ion Torrent 04-02-2013, 04:55 AM
Replies: 4
Views: 3,731
Posted By bernardo_bello
Thank you snetmcom, Now it's clear. I...

Thank you snetmcom,

Now it's clear.

I found in this paper the dUTP/UDG method explained, althoght the Ion Torrent RNA-seq library preparation is based on ligation method.
...
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