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Forum: RNA Sequencing 05-11-2012, 06:02 AM
Replies: 15
Views: 6,734
Posted By pasta
Thanks for your input sshell. Personally, I...

Thanks for your input sshell. Personally, I didn't know abt UTRs in bacteria and it explains this behaviour.
Forum: Bioinformatics 03-30-2012, 05:39 AM
Replies: 26
Views: 13,064
Posted By pasta
Thank you Jonathan for thinking about the "people...

Thank you Jonathan for thinking about the "people of the future" :)
Works like a charm !!

Antoine
Forum: RNA Sequencing 07-21-2011, 06:18 AM
Replies: 3
Views: 2,630
Posted By pasta
Hi Sang, As you do not have any intron/exon...

Hi Sang,

As you do not have any intron/exon with bacteria, I simply used Velvet and/or Edena for this purpose. Works pretty well.


toni
Forum: Bioinformatics 07-12-2011, 01:52 AM
Replies: 3
Views: 4,987
Posted By pasta
Maybe this can help:...

Maybe this can help: http://seqanswers.com/forums/showthread.php?t=4719
Forum: Bioinformatics 07-04-2011, 11:51 PM
Replies: 2
Views: 8,164
Posted By pasta
Thanks Simon for your answer. We do have 2...

Thanks Simon for your answer.
We do have 2 conditions to compare:

condition 1 : Paired-end run + Single-end run
condition 2 : Paired-end run + Single-end run

You are right, since we do not...
Forum: Bioinformatics 07-04-2011, 06:45 AM
Replies: 2
Views: 8,164
Posted By pasta
Question RNA-seq: Replicates, single-end, paired-end story

Hi,

In my lab they made a first RNA-seq run with single-ends, but because the coverage was a bit low they decided to make a new run on the same samples 6 months later, with the paired-end...
Forum: Bioinformatics 04-04-2011, 07:45 AM
Replies: 7
Views: 4,761
Posted By pasta
Well, first load your Genbank file(s) on the...

Well, first load your Genbank file(s) on the startup window:
File > Open > select your files
Then, when your chromosome is loaded, on the new window simply choose:
File > Read BAM/VCF > select...
Forum: Bioinformatics 03-25-2011, 02:42 AM
Replies: 11
Views: 3,610
Posted By pasta
*Just for the community* I also found TIGR++...

*Just for the community*
I also found TIGR++ :http://www.cbcb.umd.edu/software/pirate/tigr++.shtml

C++ class library used by several TIGR genefinders and other packages. Covers string & sequence...
Forum: Bioinformatics 03-21-2011, 02:31 AM
Replies: 11
Views: 3,610
Posted By pasta
You read my mind - thanks for your tip ! ...

You read my mind - thanks for your tip !


@Simon: Thanks but I am working on large files and I want to make it very memory efficient.
Forum: Bioinformatics 03-18-2011, 02:28 AM
Replies: 11
Views: 3,610
Posted By pasta
Thank you guys and n00c for your answer . ...

Thank you guys and n00c for your answer .

Cheers,

Toni
Forum: Bioinformatics 03-17-2011, 06:42 AM
Replies: 11
Views: 3,610
Posted By pasta
Thank you guys for your answers ;) The NCBI...

Thank you guys for your answers ;)
The NCBI toolbox is maybe a bit limited but Seqan looks pretty cool.

Thanks++

toni
Forum: Bioinformatics 03-17-2011, 03:31 AM
Replies: 11
Views: 3,610
Posted By pasta
Partially solved for SAM format: A C library is...

Partially solved for SAM format: A C library is available on SAMtools website (http://samtools.sourceforge.net/samtools-c.shtml), dumb me !!
Any other good library for Gbk, fasta and ptt ?
Forum: Bioinformatics 03-17-2011, 02:36 AM
Replies: 11
Views: 3,610
Posted By pasta
Question SOLVED - C++ libraries for NGS data and such

Hi there,

I am a Delphi/php guy and I am new using C++ in bioinformatics.
I am looking for the most mature c++ library than can deal with Next Generation Sequecing data and common file formats...
Forum: RNA Sequencing 03-15-2011, 04:53 AM
Replies: 3
Views: 2,630
Posted By pasta
Question RNA-seq: ab initio reconstruction of transcriptome with prokaryotes

Dear all,

A few programs/pipeline allow ab initio reconstruction of eukaryotic transcriptomes, such as Cufflinks or Scripture.
Do you know any software that would do the same on a RNA-seq ...
Forum: Bioinformatics 03-02-2011, 11:34 PM
Replies: 6
Views: 2,641
Posted By pasta
Ok thank you all for your feedback. It seems that...

Ok thank you all for your feedback. It seems that Geneious is more suitable for biologists than for bioinformaticians.

Thanks

antoine
Forum: Bioinformatics 02-27-2011, 11:38 PM
Replies: 6
Views: 2,641
Posted By pasta
Thank you Milkman for your feedback ;)

Thank you Milkman for your feedback ;)
Forum: Bioinformatics 02-25-2011, 07:24 AM
Replies: 12
Views: 6,692
Posted By pasta
Cuffdiff is a great tool but I stopped using it...

Cuffdiff is a great tool but I stopped using it -> too many bugs
Forum: Bioinformatics 02-17-2011, 12:31 AM
Replies: 6
Views: 2,641
Posted By pasta
Question Geneious: Any good ?

Dear all,

Has any of you tried the Geneious software for Next-Gen sequence assembly or for other applications? Is it worth paying for a software that use 70% of non-commercial sofware in its...
Forum: RNA Sequencing 02-11-2011, 05:12 AM
Replies: 15
Views: 6,734
Posted By pasta
Thank you very much for your explanations, I...

Thank you very much for your explanations, I appreciate. I am really starting to understand The Biology behind the data, if that makes sense.

Thanks again !

Toni
Forum: RNA Sequencing 02-10-2011, 11:35 PM
Replies: 15
Views: 6,734
Posted By pasta
Total RNA was treated twice with MicrobExpress...

Total RNA was treated twice with MicrobExpress (ambion) to remove most rRNA.
mRNA was fragmented to prepare cDNA with hexanucleotides as primers and RNase H was used on the other strand. Then,...
Forum: RNA Sequencing 02-10-2011, 12:47 AM
Replies: 15
Views: 6,734
Posted By pasta
Thank your for these answers, that's very nice...

Thank your for these answers, that's very nice from you. I forgot to mention that all rRNA sequences were removed from our analysis.
For case #2, I blasted the sequence : no homology found; however...
Forum: RNA Sequencing 02-09-2011, 07:46 AM
Replies: 15
Views: 6,734
Posted By pasta
John, We used YACOP which uses several ORF...

John,
We used YACOP which uses several ORF finders: Critica, Glimmer and Z-curve.
Forum: RNA Sequencing 02-09-2011, 07:16 AM
Replies: 15
Views: 6,734
Posted By pasta
Question RNA-seq read coverage questions

Hi there,

I have a question about reads coverage and RNA-seq. I am analyzing our Illumina paired-end data that we obtained from bacterial mRNA with Artemis (alignement with BWA) and I noticed some...
Forum: Bioinformatics 02-09-2011, 03:58 AM
Replies: 7
Views: 4,761
Posted By pasta
I just did something stupid with Artemis... I...

I just did something stupid with Artemis... I tried to load the BAM file straight away without any genome loaded first .... I thought it was worth mentioning I was stupid LOL
Forum: Bioinformatics 02-08-2011, 07:47 AM
Replies: 7
Views: 4,761
Posted By pasta
Forget abt my question - I just figured it out...

Forget abt my question - I just figured it out myself :)

(whaoo, it took me exactly 1 hour LOL)
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