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Forum: Illumina/Solexa 03-07-2019, 03:54 PM
Replies: 1
Views: 1,581
Posted By rexxi
Talking Is there a paired end joiner which writes also the reads before merging?

Hi, I have a weird question. But I'm looking for a software which not just merge the paired reads but also writes them in a new file.

When a software matches a pair of reads it writes them in the...
Forum: Illumina/Solexa 03-07-2019, 10:31 AM
Replies: 3
Views: 919
Posted By rexxi
Hi! thanks for your reply. Actually I asked the...

Hi! thanks for your reply. Actually I asked the reason why they didinīt performed a demultiplex propperly and they explained me that they used a protocol to improve quality and supposedly bcl2fastq...
Forum: Illumina/Solexa 03-06-2019, 12:27 PM
Replies: 3
Views: 919
Posted By rexxi
How to split fastq cointaing shared forward barcodes but different reverse ones?

Hi, I need your help because I'm completely lost with that. I received a paired-end sequencing containing many samples in a forward and reverse paired end fastq set of files as shown below.
The...
Forum: Bioinformatics 10-09-2012, 07:09 AM
Replies: 4
Views: 3,562
Posted By rexxi
Hi Jeremy, thanks for your answer... Yes I...

Hi Jeremy, thanks for your answer...

Yes I tried to use this manual, but when I was readind I didin't notice a real help. I tried to use the configuration example that appears in this site, and I...
Forum: Bioinformatics 10-08-2012, 11:35 AM
Replies: 4
Views: 3,562
Posted By rexxi
SOAPdenovo-trans without paired reads

Hi all of you,

I'm trying to configure a transcriptome sequence assembly using SOAPdenovo-trans, but I can't find a appropiate manual, my problem starts because I don't have a paired-reads...
Forum: Bioinformatics 09-14-2012, 10:35 AM
Replies: 3
Views: 4,414
Posted By rexxi
Question KO (Kegg orthology) database to download

Hi all of you, my apologies if I answer you too much times, but I make questions of a parter too.

Well my problem is that we are trying to download KO database to align it with a reads set but we...
Forum: Bioinformatics 09-14-2012, 06:19 AM
Replies: 2
Views: 4,625
Posted By rexxi
thanks you very much!. That is I need :) ...

thanks you very much!. That is I need :)

Regars,

Oscar
Forum: Bioinformatics 09-13-2012, 12:39 PM
Replies: 2
Views: 4,625
Posted By rexxi
Question SRA format file. How to use it?

I downloaded a sequencing proyect from SRA (http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi) and I downloaded a ile which contains a lot of information of raw reads. My problem starts when I try to...
Forum: Bioinformatics 08-31-2012, 12:12 PM
Replies: 1
Views: 1,084
Posted By rexxi
Question Are there tools for "de novo" assembly of rna-Seq and genomic DNA

Hi all of you,

In our laboratory, we are trying to improve the information of our sequencing data, and we have a sequencing proyect of one specie, but we have made a rna-seq by 454 and a genomic...
Forum: Bioinformatics 08-20-2012, 02:20 PM
Replies: 3
Views: 1,688
Posted By rexxi
Question Degenerate primers desing software

Hi all of you,

I'm looking for a software to design degenerate primers to make a multiplex PCR to try to close a little genome who has 10 contigs. I tried to use some primers developers softwares...
Forum: Bioinformatics 08-16-2012, 01:05 PM
Replies: 2
Views: 1,088
Posted By rexxi
where can I find a good EST anotation pipeline?

Hi, i'm trying to find a software preferently a local installation to make an EST annotation, but I can't find a dependable software. Where can I find something like this? It's for a transcriptome. ...
Forum: Bioinformatics 08-01-2012, 08:16 AM
Replies: 1
Views: 1,417
Posted By rexxi
Question how to optimize viral genome assembly in WGS 7.0?

Hi all there,

I'm reviewing another assemblers to try to get a lower number of contigs, for this I'm trying to use Celera assembler, but it gives me a lot of contigs. I was searching for...
Forum: Bioinformatics 07-12-2012, 01:37 PM
Replies: 5
Views: 4,868
Posted By rexxi
its name is bp_aacomp.pl, this script can count...

its name is bp_aacomp.pl, this script can count the aminoacids of a FASTA format file. This doesn't work good with multifasta file, because it takes count of all the aminoacids of the file. If you...
Forum: Bioinformatics 07-10-2012, 07:58 AM
Replies: 3
Views: 1,904
Posted By rexxi
Thanks for your suggest, now I'm trying to finish...

Thanks for your suggest, now I'm trying to finish this alignment, because it takes a lot of days, while I'll try the suggest of Richard Finney cutting where the alignment stops. For the next try I'll...
Forum: Bioinformatics 07-06-2012, 06:53 AM
Replies: 3
Views: 1,904
Posted By rexxi
Blast problem in metagenomics alignment

Hi there, well I presented an annoying problem with blast. The problem is the next:

We are triying to aling a metagenomic sequence project with local blast, using software packages included in...
Forum: 454 Pyrosequencing 06-13-2012, 02:11 PM
Replies: 4
Views: 1,888
Posted By rexxi
flxlex, I was reviewing your suggest, but I have...

flxlex, I was reviewing your suggest, but I have troubles whit it because in my 454ContigGraph.txt file there is not a line with the scaffolds information (and I don't have a Saccolfs file in my...
Forum: 454 Pyrosequencing 06-04-2012, 11:48 AM
Replies: 2
Views: 1,781
Posted By rexxi
Hi, your first question is related with the...

Hi, your first question is related with the quality standard used in the sequencing, 10 or lower as you told, explains a bad quality read (usually that this number can be 64) , but you have to...
Forum: 454 Pyrosequencing 06-01-2012, 12:25 PM
Replies: 4
Views: 1,888
Posted By rexxi
I was searching for a closely related reference...

I was searching for a closely related reference but I didin't find anything. And we don't have a paired end sequence data, for this I am designing primers, but as I was not as clear of the strategy...
Forum: 454 Pyrosequencing 06-01-2012, 08:36 AM
Replies: 6
Views: 2,284
Posted By rexxi
Has been released? I'm using just 2.6, if I...

Has been released? I'm using just 2.6, if I install it, I'll tell you the deiferences
Forum: 454 Pyrosequencing 06-01-2012, 08:30 AM
Replies: 4
Views: 1,888
Posted By rexxi
problems closing gaps phage genome

Hi there!,

I suscribe to this forum cause I notice that is really useful for everyone who is working un NGS technology.

Well, my trouble starts with de gap closing of a phage... there are...
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