SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 47
Search took 0.00 seconds.
Search: Posts Made By: aloliveira
Forum: Bioinformatics 07-04-2019, 12:43 AM
Replies: 0
Views: 488
Posted By aloliveira
Bug in mrbayes 3.2.6 x64 (prset popsizepr)

Hello everyone,

I have been trying to set up a multi-species coalescent run in mrbayes for quite a while and I'm starting to get crazy. Apparently there is a bug in the prset popsizepr prior that...
Forum: Bioinformatics 02-22-2016, 02:44 AM
Replies: 4
Views: 1,679
Posted By aloliveira
Thanks Kevin, I have installed TransDecoder and I...

Thanks Kevin, I have installed TransDecoder and I will give a try.
Forum: Bioinformatics 02-19-2016, 06:03 AM
Replies: 4
Views: 1,679
Posted By aloliveira
I am having the same problems. Any solution? ...

I am having the same problems. Any solution?
Thanks,
Forum: Bioinformatics 06-16-2015, 10:51 PM
Replies: 5
Views: 1,018
Posted By aloliveira
The libglib2-0 was installed via apt-get, and I...

The libglib2-0 was installed via apt-get, and I modified the make file with the following command lines:

find ./ -type f -name "makefile" -exec sed -i.old 's/glib-config --libs/pkg-config --libs...
Forum: Bioinformatics 06-16-2015, 05:34 AM
Replies: 5
Views: 1,018
Posted By aloliveira
GeneMax I'm running in Ubuntu-Linux. I already...

GeneMax I'm running in Ubuntu-Linux. I already installed that library and modified the makefile to include the libglib2.0 during the compilation, but still the error persists.
Forum: Bioinformatics 06-16-2015, 04:44 AM
Replies: 5
Views: 1,018
Posted By aloliveira
wise eternal compilation error!

Hello,

I am trying to run CEGMA, but I am not able to compile genewise in order to do so. I've followed so many different tutorials, but still I could find the answer for my problem. I am Biology...
Forum: Bioinformatics 05-07-2014, 04:22 AM
Replies: 0
Views: 975
Posted By aloliveira
Protein coding sequence in Transcriptomic data

Hello All,

I'm starting my downstream analysis with my Illumina transcriptome data. I assembled the data using three diferent assemblers (CLC, Trinity and IDBA-trans), and now I'm searching for...
Forum: Bioinformatics 02-26-2014, 08:36 AM
Replies: 1
Views: 1,139
Posted By aloliveira
Isoforms and downstream analysis

Hello,

I am very new in this transcriptome field and I have one question concerning the downstream analysis. I already assembled all my data, and now I'm preparing the data to the downstream...
Forum: Bioinformatics 02-02-2014, 02:18 AM
Replies: 2
Views: 1,410
Posted By aloliveira
So, I just solved the problem changing the...

So, I just solved the problem changing the chrysalis parameter -max_mem_reads to a lower value.

:)
Forum: Bioinformatics 02-01-2014, 08:16 AM
Replies: 2
Views: 1,410
Posted By aloliveira
More informations about the error.

More informations about the error.
Forum: Bioinformatics 02-01-2014, 08:10 AM
Replies: 2
Views: 1,410
Posted By aloliveira
Error in Trinity - Chrysalis: ReadsToTranscripts (SOLVED)

Hello,

I am running trinity to perform some de novo assemblies and everything was doing ok. Now I am facing a really weird problem that is making the trinity die everytime.



That is the...
Forum: Bioinformatics 01-30-2014, 05:37 AM
Replies: 11
Views: 2,605
Posted By aloliveira
Nuria, Maybe this website can help you. ...

Nuria,

Maybe this website can help you.

http://contig.wordpress.com/2010/04/13/newbler-output-iii-the-454contiggraph-txt-file/

Everything we need to know about newbler is there.
Best...
Forum: Bioinformatics 05-02-2012, 12:46 PM
Replies: 1
Views: 1,601
Posted By aloliveira
I don't know whats is going on, and I never used...

I don't know whats is going on, and I never used Artemis with coverage option. My guess: maybe the difference between the coverage is due to the way of the coverage was calculated. That way can be in...
Forum: Bioinformatics 04-25-2012, 09:39 AM
Replies: 3
Views: 13,293
Posted By aloliveira
Feng, How are you? There is an excelent...

Feng,


How are you? There is an excelent paper that describes the FASTQ encoding. But kmcarr is correct, all the FASTQ sequences from ncbi are Phred+33.
...
Forum: Bioinformatics 04-16-2012, 10:31 AM
Replies: 3
Views: 2,425
Posted By aloliveira
hylei, There is no such thing as "better or...

hylei,

There is no such thing as "better or worst assembler". Every one has your own advantages and disadvantages. SOAPdenovo, ABySS and Velvet are commonly used when we're dealing with...
Forum: Bioinformatics 03-20-2012, 06:38 PM
Replies: 1
Views: 1,669
Posted By aloliveira
Question on the de Bruijn Graphs

I ran a few times the Velvet, SOAP Abyss and found something intriguing (or that may be my ignorance) in all assembly. And here's my question:

1) Why two contigs which have approximately 68 base...
Forum: Bioinformatics 03-06-2012, 09:49 AM
Replies: 5
Views: 1,440
Posted By aloliveira
Looks like -max_target_seqs does not work...

Looks like -max_target_seqs does not work neither. Another solutions?
Forum: Bioinformatics 03-06-2012, 03:09 AM
Replies: 1
Views: 1,708
Posted By aloliveira
Short Read Archive - NCBI

I'm working with Illumina and 454 datasets obtained from the NCBI-SRA. And I have a question:

1) The database contains the sequences of adaptors and require a pre-processing before the assembling...
Forum: Bioinformatics 03-01-2012, 11:03 AM
Replies: 2
Views: 1,839
Posted By aloliveira
sklages, Thank you. I already signed up

sklages,

Thank you. I already signed up
Forum: Bioinformatics 03-01-2012, 10:48 AM
Replies: 2
Views: 1,839
Posted By aloliveira
Mira and non-uniform reads coverage

Hello,

i am trying to assembling datasets that have large difference in reads coverage with mira. Apparently within the MIRA there are several parameters that can improve the assembly with this...
Forum: Bioinformatics 03-01-2012, 03:35 AM
Replies: 0
Views: 1,222
Posted By aloliveira
Quality values in ace file (CAP3, Newbler and MIRA)

Hello,

I am running Newbler, Cap3 and Mira for long reads assembly. And i have just one question:

Since i have no quality file (a flat file with base qualities) for the reads (classical Phred...
Forum: Bioinformatics 02-02-2012, 02:40 AM
Replies: 11
Views: 2,605
Posted By aloliveira
Thanks, for all the aswers. The parameter -urt...

Thanks, for all the aswers. The parameter -urt reallys works for my problem. I will try also your suggestion flxlex.

André
Forum: Bioinformatics 01-31-2012, 05:03 AM
Replies: 11
Views: 2,605
Posted By aloliveira
Newbler and read coverage

Hello,

I am running Newbler under several parameters and have some questions.

1) Is there any parameter that specifies the coverage of the sample used by Newbler in the assembly process?

2)...
Forum: Bioinformatics 12-06-2011, 01:57 AM
Replies: 3
Views: 4,239
Posted By aloliveira
You can use BLAST program and specify the...

You can use BLAST program and specify the parameter -W 20 (in that way BLAST will report just the hits with at least 20 pb of similarity). Ahhh, an important think deactivate the low complexity...
Forum: Bioinformatics 12-05-2011, 04:42 AM
Replies: 10
Views: 2,998
Posted By aloliveira
Cap3 is an assembler program not an aligner...

Cap3 is an assembler program not an aligner program. If you want an alignment to the genome using EST use the program BLAT.
Showing results 1 to 25 of 47

 


All times are GMT -8. The time now is 10:47 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO