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Forum: Bioinformatics 09-23-2017, 01:54 PM
Replies: 1
Views: 860
Posted By bfantinatti
Solved

Guys, problem solved when I rebuild the references. I do not know what caused this, but now is everything ok with both systems.
Forum: Bioinformatics 09-22-2017, 07:36 PM
Replies: 1
Views: 860
Posted By bfantinatti
Bowtie2 refusing to parallelize job

Hi guys, today I had a problem that I never heard of before.
I am aligning some transcriptome samples agains different references (mammals).
At first I tried to run these alignments in a Mac pro...
Forum: Bioinformatics 07-31-2014, 11:37 AM
Replies: 4
Views: 1,540
Posted By bfantinatti
Dust

I am using DUST to perform this task.
But DUST do not remove the reads with low complexity. It put the low complexity bases in lowercase.
I don't know how to remove those lowercase reads after...
Forum: Illumina/Solexa 07-22-2014, 06:51 AM
Replies: 0
Views: 994
Posted By bfantinatti
MiRNA collapse

Hello guys, I work with microRNA illumina data, and I am having problems to collapse those reads.
I am working with reads from 17 to 25nt.
I tried to use fastx_collapser for collapse my reads...
Forum: Bioinformatics 12-11-2013, 10:06 AM
Replies: 2
Views: 1,590
Posted By bfantinatti
I am having the same problem. Some times shows...

I am having the same problem. Some times shows this error, some times shows "Segmentation fault", sometimes both errors take more time to appear, sometimes appears as soon as I start the process... I...
Forum: Bioinformatics 12-11-2013, 07:44 AM
Replies: 4
Views: 3,988
Posted By bfantinatti
Yes

Yes, I reinstalled and reformated the database several times.
Using the nt database downloaded from ncbi, it works perfectly. Formating my own database based on a genome I have, if worked perfectly...
Forum: Bioinformatics 12-10-2013, 04:06 AM
Replies: 4
Views: 3,988
Posted By bfantinatti
Blast2 - Segmentation Fault

Hi guys,
I am having a problem with blast2.
I am running linux mint 14, and installed blast2 using the repository.
It worked fine once, but after the first usage, started to present the following...
Forum: Bioinformatics 10-02-2013, 04:40 AM
Replies: 1
Views: 2,502
Posted By bfantinatti
Hello

Hello hsmart, I think you have a compilation problem. Did you compile this program, or just used the executables that came inside the src folder? If you are using these files, I suggest to compile...
Forum: Bioinformatics 09-19-2013, 07:36 AM
Replies: 2
Views: 2,245
Posted By bfantinatti
MiRExpress

Hello,
I am starting to use mirexpress to extract expression profiles from various samples too.
For using the Trim-adaptor script, we have to create a text file containing the adaptor sequence,...
Forum: Bioinformatics 09-17-2013, 11:11 AM
Replies: 2
Views: 1,631
Posted By bfantinatti
Hello sdriscoll, in fact the values are integers....

Hello sdriscoll, in fact the values are integers. I tested with other sequence data, and is all the same... Integers.
I saw something about a R package to work with this. I will take a look and post...
Forum: Bioinformatics 07-22-2013, 05:58 AM
Replies: 2
Views: 1,631
Posted By bfantinatti
Analyzing miRNA data using MirExpress

Hello guys,
I have to compare two datasets of miRNA sequencing (Illumina data). I installed and ran mirexpress for the two datasets.
Is there any way to compare the results? I intend to observe the...
Forum: Bioinformatics 05-03-2013, 04:44 AM
Replies: 2
Views: 1,191
Posted By bfantinatti
Thank you

Thank you a lot Rachel, I wiil take a look :)
Forum: Bioinformatics 05-02-2013, 06:42 PM
Replies: 2
Views: 1,191
Posted By bfantinatti
miRNa sequencing and comparision

Hello guys,
I have a project in which I intend to analyse miRNAs from various tissues between two different groups. Ex: To compare liver miRNAs from group 1 against liver miRNAs from groups 2 (both...
Forum: Bioinformatics 11-20-2012, 05:55 AM
Replies: 19
Views: 4,430
Posted By bfantinatti
No

I still did not solve the problem, Hiroki.
My problem is in this moment to create a admin account. I have already added my e-mail to the configuration file and nothing happens. I still can not log...
Forum: Bioinformatics 11-08-2012, 08:51 AM
Replies: 19
Views: 4,430
Posted By bfantinatti
Problem

Hey guys, I have already added my user e-mail on that list as both you said, reloaded the server (sh run.sh --reload) and then 127.0.0.1:8080 on by browser. Nothing different happened. I couldn't...
Forum: Bioinformatics 11-08-2012, 04:56 AM
Replies: 19
Views: 4,430
Posted By bfantinatti
Admin privileges

I was looking for information about how to get admin privileges, and didn't found a solution yet. I'll keep looking. If I do not find, I come back here to ask for help. Thank you a lot.
(I am new on...
Forum: Bioinformatics 11-07-2012, 05:36 AM
Replies: 19
Views: 4,430
Posted By bfantinatti
Add large bam files to Galaxy

Hi guys,
I installed a Galaxy instance on my computer (it is a Mac Pro, 12 GB Ram, 2.6 GHz quad core intel Xeon). I start the server on the terminal, and them I type on my browse the address...
Forum: Bioinformatics 11-07-2012, 03:42 AM
Replies: 7
Views: 2,943
Posted By bfantinatti
Yes

Hello dnusol, yes i did. Sorry, I forgot to post the solution here. I got the solution on annother forum related to bash issues.
The solution was to apply the following code:

awk '($2-p2)>1{...
Forum: Bioinformatics 08-27-2012, 10:01 AM
Replies: 7
Views: 2,943
Posted By bfantinatti
Hello

I tried using -A and worked very well :) Thank you for the answer.
One more question:
When I have some gap on assembly, mpileup jumps directly to the next position presenting a coverage:...
Forum: Bioinformatics 08-27-2012, 07:10 AM
Replies: 7
Views: 2,943
Posted By bfantinatti
Hello

I used pipe awk and worked very well, thank you for the two answers.
Despite generated the files as I wanted, I detected a little problem in results.
The columns of the coverage shows some wrong...
Forum: Bioinformatics 08-22-2012, 11:08 AM
Replies: 7
Views: 2,943
Posted By bfantinatti
Mpileup output

Hello!
I'm using "mpileup -p reference.fasta my_file.bam" to generate a file that gives me the coverage for each base. This command generates a file with 6 columns but only the column 1, 2 and 4...
Forum: Bioinformatics 08-21-2012, 11:02 AM
Replies: 5
Views: 7,296
Posted By bfantinatti
Different values

Hello there, I had the same problem, and previous posts solved my problems. But there is an little detail:
I have a bam file, and used mpileup to list the per position coverage. Resulted in a file...
Showing results 1 to 22 of 22

 


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