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Search: Posts Made By: mattia
Forum: Bioinformatics 07-16-2014, 04:12 AM
Replies: 3
Views: 944
Posted By mattia
What kind of species are you studying? Maybe...

What kind of species are you studying?
Maybe the error has been generated due to the reference length.

As the message suggest you:
1) cut the reference in 2 different .fasta files;
2) create...
Forum: Bioinformatics 05-29-2014, 02:30 AM
Replies: 0
Views: 1,033
Posted By mattia
Question Exon locations in Novel Transcripts

Hi,
I found several novel transcripts using RNA-Seq data (paired-end reads), in intergenic regions. Some of them have 2 or 3 exons.
Now I have:
1) a BED file with chromosome location of entire...
Forum: Bioinformatics 04-15-2014, 07:38 AM
Replies: 7
Views: 5,281
Posted By mattia
I have the same kind of error: I've tried to...

I have the same kind of error: I've tried to launch cufflink 2.2.0 with the same parameters of previous versions (using a bam file already analyzed!!!), and a "segmentation fault" error occurred.
...
Forum: Bioinformatics 07-12-2013, 08:25 AM
Replies: 10
Views: 1,944
Posted By mattia
If you want to have a little number of reads...

If you want to have a little number of reads (suppose you have a .fastq file) in your "test sample", an easy way is :


One read = 4 rows in .fastq....so, in order to have (for example!!) 2500...
Forum: Bioinformatics 06-07-2013, 07:34 AM
Replies: 3
Views: 5,862
Posted By mattia
log(zero)=-inf I think you have 0 as a mean...

log(zero)=-inf

I think you have 0 as a mean value (between replicates) in first condition (eg Treatment) and a number as mean value (between replicates) in the second condition(eg Control), so:...
Forum: Bioinformatics 05-31-2013, 08:02 AM
Replies: 6
Views: 1,464
Posted By mattia
In my opinion the problem is not "how cufflinks...

In my opinion the problem is not "how cufflinks (cuffdiff for DE) works": I'm using Cufflinks and it works very good.
I suggest to use always (either using Cufflinks and HTS-count, edgeR,....)...
Forum: Bioinformatics 05-31-2013, 06:28 AM
Replies: 6
Views: 1,464
Posted By mattia
I suppose it could be an annotation problem: as...

I suppose it could be an annotation problem: as you can see in figure in attach, for the same gene you can have different exons length (choosing different annotation). So, different transcript length...
Forum: Bioinformatics 05-21-2013, 03:53 AM
Replies: 11
Views: 4,433
Posted By mattia
As you can see in my previous post...

As you can see in my previous post (http://seqanswers.com/forums/showthread.php?t=29981), I solve this problem just by "unsetting" -p parameter.
Forum: Bioinformatics 05-15-2013, 02:17 AM
Replies: 8
Views: 3,658
Posted By mattia
Thumbs up SOLVED!!! Tophat2.0.8b segment-junc err=1

I solve my problem: I suppose it can be a bug (in all tophat 2.0.x versions). You have not to set -p parameter. In this way Tophat works correctly, but, obviously, it takes too long!!!!
For...
Forum: Bioinformatics 05-09-2013, 08:34 AM
Replies: 6
Views: 2,075
Posted By mattia
I cannot answer about edgeR, 'cause I've never...

I cannot answer about edgeR, 'cause I've never used it but I'm quite sure that Deseq is able to work also without replicates.
Forum: Bioinformatics 05-09-2013, 05:28 AM
Replies: 6
Views: 2,075
Posted By mattia
I suppose you have to take in account two things:...

I suppose you have to take in account two things:
1 - Variance between replicates;
2 - Number of replicates.

Generally, a statistical test gives you a significant p-value if the number of...
Forum: Bioinformatics 05-08-2013, 08:12 AM
Replies: 7
Views: 10,082
Posted By mattia
Try with Ensebl tool...

Try with Ensebl tool (http://www.ensembl.org/downloads.html)
-->
Click on "customise your download".
Then select "ENSEMBL GENES 71 " and your species.
Now, appears : "Filter"s and "Attributes"....
Forum: Bioinformatics 05-08-2013, 07:14 AM
Replies: 8
Views: 3,658
Posted By mattia
I check: All my reads are OK, but the problem...

I check: All my reads are OK, but the problem still remains.
Forum: Bioinformatics 05-08-2013, 02:38 AM
Replies: 8
Views: 3,658
Posted By mattia
ok, I can check but I'm doubtful yet; I tested...

ok, I can check but I'm doubtful yet; I tested Tophat2, by using the same input file I've already aligned with Tophat1 (without any problem).
Forum: RNA Sequencing 05-07-2013, 02:25 AM
Replies: 1
Views: 1,425
Posted By mattia
Question Tophat2.0.8b segment-junc err=1

Hi,
Last week I upgraded last version of Tophat; so now I'm using Tophat 2.0.8b with bowtie 1.0.0 (I need to align color space reads).
Before I used Tophat 1.4.1 and bowtie 0.12.8, and I never...
Forum: Bioinformatics 05-07-2013, 02:24 AM
Replies: 8
Views: 3,658
Posted By mattia
Thumbs up SOLVED!!! Tophat2.0.8b segment-junc err=1

Hi,
Last week I upgraded last version of Tophat; so now I'm using Tophat 2.0.8b with bowtie 1.0.0 (I need to align color space reads).
Before I used Tophat 1.4.1 and bowtie 0.12.8, and I never...
Forum: Bioinformatics 12-18-2012, 12:33 AM
Replies: 6
Views: 5,059
Posted By mattia
;) ok I solve my problem; in particular (for...

;) ok I solve my problem; in particular (for other users):
You have to:
tar -zxvf eigen-eigen-5097c01bcdc4.tar.gz; (for actual eigen package: version 3.1.2)
cd eigen-eigen-5097c01bcdc4;
mkdir...
Forum: Bioinformatics 12-17-2012, 08:27 AM
Replies: 6
Views: 5,059
Posted By mattia
:eek::eek: I have not "include" directory in...

:eek::eek: I have not "include" directory in ../../eigen-eigen-5097c01bcdc4/Eigen

So, do i have to create ../../eigen-eigen-5097c01bcdc4/Eigen/include and put all files in it?????

my directory...
Forum: Bioinformatics 12-17-2012, 08:06 AM
Replies: 6
Views: 5,059
Posted By mattia
Yes, I compiled eigen in this way: mkdir...

Yes, I compiled eigen in this way:

mkdir /home/software_analisi/altri_software/Eigen/bin
cd /home/software_analisi/altri_software/Eigen/bin...
Forum: RNA Sequencing 12-17-2012, 06:51 AM
Replies: 0
Views: 2,225
Posted By mattia
Question Cufflinks 2 - error message

Hi,
I'm trying to install Cufflink2.0.2 in order to compare new version and "old" version (1.3.0) and to upgrade my pipeline. I type:

./configure --prefix=$HOME/path/to/my/Cufflinks2/dir...
Forum: Bioinformatics 12-17-2012, 06:49 AM
Replies: 6
Views: 5,059
Posted By mattia
Question Cufflinks 2 - install error

Hi,
I'm trying to install Cufflink2.0.2 in order to compare new version and "old" version (1.3.0) and to upgrade my pipeline. I type:

./configure --prefix=$HOME/path/to/my/Cufflinks2/dir...
Forum: RNA Sequencing 11-14-2012, 02:43 AM
Replies: 0
Views: 1,091
Posted By mattia
Tophat and Mapping QV

Hi,
I'm using TopHat v1.4.1 in order to analyze paired-end reads (75-35) in color space.
My tipical command line is:
tophat -G $annotation_file -C --no-coverage-search --library-type...
Forum: Bioinformatics 11-14-2012, 02:28 AM
Replies: 0
Views: 1,107
Posted By mattia
TopHat and mapping QV

Hi,
I'm using TopHat v1.4.1 in order to analyze paired-end reads (75-35) in color space (RNA-Seq analysis).
My tipical command line is:
tophat -G $annotation_file -C --no-coverage-search...
Forum: Bioinformatics 04-24-2012, 03:50 AM
Replies: 1
Views: 1,504
Posted By mattia
cufflinks configuration

Hi,
I'm trying to define the best options configuration of Cufflinks. In order to estimate only known transcripts, is my command-line right or do I have to modify something?

cufflinks -u...
Forum: Bioinformatics 04-17-2012, 02:00 AM
Replies: 0
Views: 2,399
Posted By mattia
Best reads normalization in RNA-Seq

Hi, I'm analysing a bit of RNA-Seq data, in particular at the moment I try to compare the expression of genes in several conditions. To evaluate the expression value I used both FPKM value (Cufflinks...
Showing results 1 to 25 of 30

 


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