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Forum: Bioinformatics 05-19-2012, 08:25 PM
Replies: 0
Views: 1,933
Posted By detq182
Post Comparison of Tissue specific expression (Rna-seq)

Hi

I'm wondering if exist a easy method to identify Tissue specific expression using the result of RNA-seq approach, i have 4 condition and i want to compare one to another.

What program could...
Forum: Bioinformatics 04-18-2012, 09:00 AM
Replies: 9
Views: 4,490
Posted By detq182
thanks

Im going to try that
Forum: Bioinformatics 04-17-2012, 06:13 PM
Replies: 9
Views: 4,490
Posted By detq182
Post Im sorry if i dont show some initiative in...

Im sorry if i dont show some initiative in solving my problem, im in finals on the college and i started just a few days ago learning "Unix and Perl Primer for Biologists", im new in this just 2...
Forum: Bioinformatics 04-15-2012, 06:17 AM
Replies: 4
Views: 2,264
Posted By detq182
please some help here. i have a big problem...

please some help here.

i have a big problem i just cant make with bioperl this;
>CL56Contig1 Nascent polypeptide associated complex alpha...
Forum: Bioinformatics 04-15-2012, 05:38 AM
Replies: 4
Views: 2,264
Posted By detq182
hi could you be more specific? im starting...

hi
could you be more specific? im starting with perl.
Forum: Bioinformatics 04-14-2012, 05:55 PM
Replies: 4
Views: 2,264
Posted By detq182
Post Make Multi-fasta with annotations

Hi everyone

Im ending my work and i have a problem, how can i make that my multi-fasta file with the query sequence has a descriptions using the annotations hits that i get from blast, here is...
Forum: Bioinformatics 04-14-2012, 05:30 PM
Replies: 9
Views: 4,490
Posted By detq182
anyone try to make a Db with the...

anyone try to make a Db with the description+sequence?
Forum: Bioinformatics 04-14-2012, 06:50 AM
Replies: 9
Views: 4,490
Posted By detq182
using perl

Im using a perl script but i cant get the original query (cDNA) insted im getting out the the protein query (blastx), i don want the protein sequence.

#!/usr/bin/perl
use Bio::SearchIO;...
Forum: Bioinformatics 04-14-2012, 04:43 AM
Replies: 9
Views: 4,490
Posted By detq182
Any sugestion

Please help me with that:(
Forum: Bioinformatics 04-13-2012, 12:35 PM
Replies: 9
Views: 4,490
Posted By detq182
Smile Make my own blast DB

Hi everyone

I have a question about how to make my own BLASTdb using the result of my Ref-seq work before the annotation step, i mean not like this

>CL1Contig1...
Forum: Bioinformatics 02-29-2012, 03:57 PM
Replies: 0
Views: 1,923
Posted By detq182
Post Fishers Exact test blast2go

Hi

i dont know how to compare 2 library of gene, cant understand if the IDs of the 2 library goes on the same txt file or in diferents file, and the refence txt file where do i get it?
the txt...
Forum: Bioinformatics 02-06-2012, 04:50 AM
Replies: 3
Views: 1,588
Posted By detq182
Thank you, work.

Thank you, work.
Forum: Bioinformatics 02-05-2012, 07:36 AM
Replies: 3
Views: 1,588
Posted By detq182
Post Bioperl output file

Hi everyone
i need some help in this script

#!/usr/bin/perl
use Bio::SearchIO;

$report_obj = new Bio::SearchIO(-format => 'blast',
...
Forum: Bioinformatics 02-04-2012, 05:12 AM
Replies: 3
Views: 3,616
Posted By detq182
Unhappy Custom local blast results

how can i custom local blast results like the threshole of the E-value and make it lower.

thank all.
Forum: Bioinformatics 02-02-2012, 02:33 PM
Replies: 22
Views: 8,917
Posted By detq182
I finally can do it comman line: ...

I finally can do it

comman line:
makeblastdb -in \blast-2.2.25+\db\uniprot_sprot.fasta -parse_seqids -dbtype prot

and done, thank all of you for your time.
Forum: Bioinformatics 02-02-2012, 06:31 AM
Replies: 22
Views: 8,917
Posted By detq182
Yes im on windows and natively not using cygwin. ...

Yes im on windows and natively not using cygwin.

please help.....
Forum: Bioinformatics 02-02-2012, 06:28 AM
Replies: 22
Views: 8,917
Posted By detq182
Cant do the command line. head command dont...

Cant do the command line. head command dont recognise.
Forum: Bioinformatics 02-02-2012, 02:55 AM
Replies: 22
Views: 8,917
Posted By detq182
thanks Kennels, but how can i check it ? the ...

thanks Kennels, but how can i check it ? the downloaded sequences said Arabidopsis_thaliana.Protein.fasta
Forum: Bioinformatics 02-01-2012, 06:22 PM
Replies: 22
Views: 8,917
Posted By detq182
Makeblastdb problem

i just download a secuence in .FASTA format from uniprot but
i cant make it work, this are the errors.

makeblastdb -in Arabidopsis_thaliana.fas -parse_seqids -dbtype prot
BLAST Database error:...
Forum: Bioinformatics 02-01-2012, 10:31 AM
Replies: 2
Views: 1,156
Posted By detq182
Question Protein data base with blast+

Hi everyone.

im new in this forum and my problem is that i download a database from ncbi with tar.gz format them extract it on /db/ and use

blastx -query Lib1_consensus_tgicl_NT_nohit.fasta...
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