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Forum: Bioinformatics 11-02-2016, 12:07 AM
Replies: 1
Views: 476
Posted By papori
DAVID significant cluster, with non significant cluster

Hi all,
I used David for RNA seq analysis and i am confused by understanding its output.
The input for David is a list of gene symbol and the output for the clustering analysis is this for example:...
Forum: General 02-10-2016, 11:50 PM
Replies: 1
Views: 551
Posted By papori
BRCA sub type information in TCGA

Hi,
I am looking for the Breast Cancer molecular subtype information in TCGA.
I searched in the clinical data files, but i havnt found it there.
What I found is "stageing" and the...
Forum: Bioinformatics 02-08-2016, 02:34 AM
Replies: 0
Views: 418
Posted By papori
TCGA level 3 SNP array names meaning

Hi all,
Do you know what is the meaning of the names?
For example:
TAKEN_p_TCGAb_379_400_FFPE_NSP_GenomeWideSNP_6_D09_1513182.hg19.seg.txt...
Forum: Bioinformatics 12-15-2015, 02:29 AM
Replies: 4
Views: 936
Posted By papori
Hi! great! i think... ;) What i understand...

Hi! great! i think... ;)

What i understand from this format is that if the "Segment_Mean" negative, there is assuming for "loss", and if its possitive assuming for "gain".
If i will...
Forum: Bioinformatics 12-14-2015, 11:58 AM
Replies: 4
Views: 936
Posted By papori
Thanks! but i need the Copy number alterations...

Thanks! but i need the Copy number alterations for aggregated/segmented regions, per sample, and not the SNP data..
Forum: Bioinformatics 12-14-2015, 11:37 AM
Replies: 0
Views: 515
Posted By papori
converting from HG19_broad_variant to GRCh37-lite

Hi all!

Is there a way to convert the HG19_broad_variant to GRCh37-lite?

I wrote algorithm that is semi automated and works only by the coordinate of the GRCh37-lite for now.

Thanks,
Pap
Forum: Bioinformatics 12-14-2015, 10:44 AM
Replies: 4
Views: 936
Posted By papori
CNV from TCGA level 3

Hi all!
I am looking for CNV public profiles for the TCGA data to use as a reference.
Do you know if there are TCGA level 3 copy number profiles that available for more than GBM, OV and LUSC?
...
Forum: Bioinformatics 12-03-2015, 02:14 AM
Replies: 3
Views: 617
Posted By papori
Thanks lindenb! I saw your post before,but i...

Thanks lindenb!
I saw your post before,but i have there a compliation error and our system admin is not in the area.. so we cant install anything right now..
The error is about the "Requires ...
Forum: Bioinformatics 12-03-2015, 12:08 AM
Replies: 3
Views: 617
Posted By papori
Linux based enzyme restriction tool

Hi all,
I guess that the answer should be simple, but honestly i googled it and didnt find the answe...
What im looking for is linux based tool to recognize enzyme restriction sites:
1) over the...
Forum: General 10-14-2015, 12:51 PM
Replies: 4
Views: 940
Posted By papori
Hi Friedrich , Did u try the data from the...

Hi Friedrich ,
Did u try the data from the TCGA?
i know there is alot of clinical data.
Cheers
Forum: Bioinformatics 07-15-2015, 01:07 PM
Replies: 6
Views: 936
Posted By papori
ohh cool! Thanks!! I like bedtools! :)

ohh cool!
Thanks!! I like bedtools! :)
Forum: Bioinformatics 07-14-2015, 01:59 AM
Replies: 6
Views: 936
Posted By papori
Ok, he didnt answer me yet.. In the meanwhile,...

Ok, he didnt answer me yet..
In the meanwhile, can u reccomened on a easy to execute tool for exploring the read depth over the human genome?
Thanks,
Pap
Forum: Bioinformatics 07-13-2015, 04:15 AM
Replies: 6
Views: 936
Posted By papori
Hi GenoMax, Yes, i saw this already and it's...

Hi GenoMax,
Yes, i saw this already and it's not detailed enough, at least for me..
I sent email to the author and waiting for his response..
I was sure that every package in R must have vignette/...
Forum: Bioinformatics 07-13-2015, 03:51 AM
Replies: 6
Views: 936
Posted By papori
Any ideas for how to use this package? Thanks, ...

Any ideas for how to use this package?
Thanks,
Pap
Forum: Bioinformatics 07-09-2015, 05:28 AM
Replies: 6
Views: 936
Posted By papori
ReadDepth manual or example

Hi all,
Do u know where can i find the manual or normal example of ReadDepth tool?
not the same example as here:
https://github.com/chrisamiller/readdepth
Its not detailed enough...
it R...
Forum: De novo discovery 07-04-2015, 10:02 AM
Replies: 2
Views: 1,380
Posted By papori
Any ideas? I will make it simpler.. How to...

Any ideas?
I will make it simpler..
How to have functional annotation when you have more than 1 orgaism in your data?
Now im using David, but its limit to single organism..
Thanks!
Pap
Forum: De novo discovery 06-25-2015, 01:23 AM
Replies: 2
Views: 1,380
Posted By papori
Functional analysis - not per organism, for de novo assembly

Hi all,
We sequenced a non model organism transcriptome and we used Trintiy for de novo assembly. Trinity generated 182,171 contigs.

Next, we annotated Trinity contigs using blastx against the...
Forum: Bioinformatics 06-24-2015, 01:30 AM
Replies: 4
Views: 574
Posted By papori
Thanks Genomax, I tried curl and it also didnt...

Thanks Genomax,
I tried curl and it also didnt work.
I think our server ftp protocol is too old....
I am trying to download in different computer..
Thanks,
Pap
Forum: Bioinformatics 06-21-2015, 11:35 PM
Replies: 4
Views: 574
Posted By papori
Hi GenoMax! I tried both: --no-passive-ftp...

Hi GenoMax!

I tried both:
--no-passive-ftp
--retry-connrefused --waitretry=30

and still the same problem..
Forum: Bioinformatics 06-21-2015, 03:13 PM
Replies: 4
Views: 574
Posted By papori
Downloading TrEMBL

Hi all,
Does anyone know why when im trying to download from uniprot
http://www.uniprot.org/downloads
the TrEMBL dataset with wget like this:
wget...
Forum: Bioinformatics 12-16-2014, 12:10 AM
Replies: 1
Views: 735
Posted By papori
Alternatives to Nature brief communication

Hi all,
I am not sure that this is the right forum for my questions, but i will try..

We wrote a brief communication paper and we sent it to Nature Methods, and it was rejected..
Now, we are...
Forum: Bioinformatics 11-25-2014, 06:02 AM
Replies: 6
Views: 883
Posted By papori
Thanks rhinoceros. This is the link that i...

Thanks rhinoceros.
This is the link that i shared also.
Did you try it?

My data is not expression.. its DNA
Forum: Bioinformatics 11-25-2014, 03:10 AM
Replies: 6
Views: 883
Posted By papori
Maybe the previous post was not clear. I am...

Maybe the previous post was not clear.
I am jist looking for any ideas on how to compare 2 heatmaps?

Thanks,
Pap
Forum: Bioinformatics 11-25-2014, 02:31 AM
Replies: 7
Views: 962
Posted By papori
Thanks GenoMax!

Thanks GenoMax!
Forum: Bioinformatics 11-24-2014, 11:31 PM
Replies: 7
Views: 962
Posted By papori
Thanks!!! this is exactly what i looked for! ...

Thanks!!! this is exactly what i looked for!

I downlod the file and these are the first 6 lines:

591 chr1 879822 879830 SAMD11:miR-504 90 +
591 chr1 900599 900606 KLHL17:miR-299/299-3p 26 +...
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