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Search: Posts Made By: mlacencio
Forum: Bioinformatics 02-24-2015, 11:59 AM
Replies: 7
Views: 1,373
Posted By mlacencio
Thank you for the answers! I will follow...

Thank you for the answers!

I will follow your suggestions to try to solve this issue.

Still regarding RNA-seq, in this same set of contigs I got some pairs of contigs that were annotated with...
Forum: Bioinformatics 02-24-2015, 03:29 AM
Replies: 7
Views: 1,373
Posted By mlacencio
First, I want to find the differentially...

First, I want to find the differentially expressed transcripts between two different conditions. Second, I want to assign to these transcripts gene ontology terms -- using blast2go or Argot2 -- to...
Forum: Bioinformatics 02-23-2015, 05:35 PM
Replies: 7
Views: 1,373
Posted By mlacencio
Hi alezhe! Can CAP3 (or another assembler)...

Hi alezhe!

Can CAP3 (or another assembler) work in my case considering that these transcripts are non-overlapping? When I used "Blast 2 sequences" to align these transcripts, no significant...
Forum: Bioinformatics 02-23-2015, 11:49 AM
Replies: 7
Views: 1,373
Posted By mlacencio
RNA-seq: different fragments from same transcript?

Hi everyone!

I got trapped in the following situation: I have some pairs of transcripts obtained by RNA-seq that were annotated with same terms, e.g. contigs A and B were annotated as 2-alkenal...
Forum: Bioinformatics 02-03-2015, 05:50 PM
Replies: 5
Views: 1,341
Posted By mlacencio
Hi Brian and GenoMax! The Blast alignments I...

Hi Brian and GenoMax!

The Blast alignments I posted are of the transcriptome to itself. Anyway, transcripts are from a tetraploid organism.

GenoMax, the sequences have been assembled by someone...
Forum: Bioinformatics 02-03-2015, 03:06 PM
Replies: 5
Views: 1,341
Posted By mlacencio
How can I distinguish assembly error from true splice or isoforms in RNA-seq?

Hii everyone!

I have received thousands of transcripts generated by a non-stranded RNA-seq and I have just annotated them (I used a in-house bash script to extract from blast results xml the most...
Forum: Bioinformatics 02-02-2015, 11:34 AM
Replies: 5
Views: 2,670
Posted By mlacencio
Kopi-o and GenoMax, Thank you for your...

Kopi-o and GenoMax,

Thank you for your answers.

So, if I use a non-stranded protocol to generate my RNA-seq library and after sequencing and assembling I discover that some pairs of my...
Forum: Bioinformatics 01-29-2015, 04:37 AM
Replies: 5
Views: 2,670
Posted By mlacencio
Dear GenoMax, In fact, other people prepared...

Dear GenoMax,

In fact, other people prepared the library. I am only the "bioinformatics guy"! But, anyway, they didn't follow a stranded library protocol. They used the TruSeq RNA Sample...
Forum: Bioinformatics 01-28-2015, 05:05 AM
Replies: 5
Views: 2,670
Posted By mlacencio
Blastx to associate GO term to transcripts

Hi everyone!

I think no one has replied me so far because I have made my question hard to understand. So, I'll try to simplify it now!

Let's suppose I have the following transcript assembled...
Forum: Bioinformatics 01-21-2015, 11:35 AM
Replies: 5
Views: 2,670
Posted By mlacencio
Is blastx reliable enough to annotate transcripts from RNA-seq?

Hi everybody!

I am a newbie on in silico functional annotation of transcripts assembled from reads produced by RNA-seq. My doubt is about the utilization of blastx for this purpose.

Many...
Forum: General 10-27-2013, 04:15 PM
Replies: 3
Views: 3,667
Posted By mlacencio
Hi Chipper! Thank you for your reply! ...

Hi Chipper! Thank you for your reply!

Actually my main concern is about the number of PCR cycles. It is known that the quantification of PCR products is unreliable if PCR reaches its saturation...
Forum: General 10-26-2013, 11:53 AM
Replies: 3
Views: 3,667
Posted By mlacencio
RNA-seq: concern about quantification of transcriptome

Hi everybody!

I'd like to generate and quantify whole transcriptomes by using RNA-seq in the near -- well, not so near -- future but I am completely newbie on this method.

My doubt concerns...
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