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Search: Posts Made By: angel-sakura
Forum: Bioinformatics 10-01-2015, 04:19 PM
Replies: 8
Views: 2,368
Posted By angel-sakura
Yes! I understand it now!! lol Thank you so...

Yes! I understand it now!! lol

Thank you so much!
Forum: Bioinformatics 10-01-2015, 05:02 AM
Replies: 8
Views: 2,368
Posted By angel-sakura
The problem is solved!! The "value" doesn't...

The problem is solved!!
The "value" doesn't need the quotation mark!
Forum: Bioinformatics 10-01-2015, 04:54 AM
Replies: 8
Views: 2,368
Posted By angel-sakura
Thank you very much!!! It is working now!!

Thank you very much!!!
It is working now!!
Forum: Bioinformatics 09-30-2015, 04:03 AM
Replies: 8
Views: 2,368
Posted By angel-sakura
Thank you very much for your reply. I'm pretty...

Thank you very much for your reply.
I'm pretty sure it is not the problem of typo, as it was working with the example data with the same commands.
Forum: Bioinformatics 09-29-2015, 11:26 PM
Replies: 8
Views: 2,368
Posted By angel-sakura
Smile problem with biomart---give 0 results

Hi everyone:

I'm trying to convert ensembl-peptide-id to GO-id with biomart. However, when I was using the following command to run it, I got 0 results.

Here are commands I was using:
ensembl...
Forum: General 05-19-2015, 03:58 AM
Replies: 2
Views: 2,369
Posted By angel-sakura
Thank you very much!! That's is what I want ...

Thank you very much!!
That's is what I want

Cheers
Forum: General 05-18-2015, 08:25 PM
Replies: 2
Views: 2,369
Posted By angel-sakura
Smile how to check the primers specificity in a local computer

Could someone please tell me how to check the specificity of primers in a local computer? I know there are lots of online tools available, i.e. primer-blast. However, the database of my research...
Forum: Bioinformatics 03-17-2015, 10:49 PM
Replies: 2
Views: 1,376
Posted By angel-sakura
Thank you very much for your reply. Yes, it's a...

Thank you very much for your reply.
Yes, it's a long gene. But even if I use some genes with normal size, I still get this error. I could give you another example:

ERROR 28: Incorrect order for...
Forum: Bioinformatics 03-15-2015, 06:24 PM
Replies: 2
Views: 1,376
Posted By angel-sakura
Smile TrainGlimmerHMM error 28 Incorrect order for exon coordinates

I try to use trainGlimmerHMM to train my data, I got this error : ERROR 28: Incorrect order for exon coordinates: gene scaffold104. Bad line: scaffold104 20180913 20180770

So I checked this genes...
Forum: Bioinformatics 01-04-2015, 02:04 AM
Replies: 1
Views: 2,741
Posted By angel-sakura
Post Gviz problem---too many stacks to draw

Hi everyone, I have encountered a problem when I was plotting my data with Gviz. The error is:Too many stacks to draw. Either increase the device size or limit the drawing to a smaller region. Could...
Forum: General 01-02-2015, 09:24 PM
Replies: 6
Views: 3,150
Posted By angel-sakura
Hi, sorry for the late reply, I was on holidays....

Hi, sorry for the late reply, I was on holidays. :)
Check this link:http://sourceforge.net/projects/plek/files/
You can downloand the PLEK and its manual from above link. The PLEK is straight...
Forum: Bioinformatics 12-21-2014, 08:52 PM
Replies: 0
Views: 1,261
Posted By angel-sakura
how to find correlation between a gene and a set of genes from one replicate RNASEQ

Hi everyone, I would like to find noval regulatory lncRNAs closed to the gene of my interest. Currently, I have found thousands of lncRNAs located within 500KB upstream and downstream of the gene of...
Forum: General 12-08-2014, 02:45 PM
Replies: 3
Views: 1,607
Posted By angel-sakura
Thank you very much !

Thank you very much !
Forum: General 12-08-2014, 05:42 AM
Replies: 3
Views: 1,607
Posted By angel-sakura
problem of creating vector in R

Hi everyone:

I have encountered a problem of creating this type of vector in R:
The format is below:
> str(geneList)
Named num [1:12495] 4.57 4.51 4.42 4.14 3.88 ...
- attr(*, "names")= chr...
Forum: Bioinformatics 12-03-2014, 02:56 PM
Replies: 15
Views: 8,361
Posted By angel-sakura
Thank you ! Now I get it working. Cheers

Thank you ! Now I get it working.

Cheers
Forum: General 12-02-2014, 04:47 AM
Replies: 6
Views: 3,150
Posted By angel-sakura
lol, I haven't done this before either, but it is...

lol, I haven't done this before either, but it is worth trying it.
Thank you !
Forum: Bioinformatics 12-02-2014, 04:45 AM
Replies: 15
Views: 8,361
Posted By angel-sakura
Sorry about my carelessness, I just focused on...

Sorry about my carelessness, I just focused on the scripts when I read the manual.
From the example data(geneList), geneList seems to contain two values, one is entrez Id, what about the other one?...
Forum: Bioinformatics 12-01-2014, 08:54 PM
Replies: 15
Views: 8,361
Posted By angel-sakura
Hi, I'm currently using clusterProfiler for GO...

Hi, I'm currently using clusterProfiler for GO enrichment analysis. It is a great tool but I have encountered a problem of inputing data. I read through the manual and find nothing about how to input...
Forum: General 12-01-2014, 02:22 AM
Replies: 6
Views: 3,150
Posted By angel-sakura
Thank you very much for your kind reply! Could...

Thank you very much for your kind reply!
Could you also recommend some commands or softwares that I can use to transfer lncRNAs (fasta format) into BED or GTF format?
Forum: General 11-30-2014, 03:38 AM
Replies: 6
Views: 3,150
Posted By angel-sakura
how to visualize locations of lncRNA close to my gene of interest

Hi, everyone, I am looking for the lncRNAs of some specific genes.
Q1: Now I have extracted all predicted lncRNAs (using PLEK) that close to my target genes (500 KB upstream or downstream). I can...
Forum: Bioinformatics 11-13-2014, 06:36 PM
Replies: 4
Views: 1,208
Posted By angel-sakura
That is what I need, a name of command. ...

That is what I need, a name of command.

Thank you very much !!
Forum: Bioinformatics 11-13-2014, 05:25 PM
Replies: 4
Views: 1,208
Posted By angel-sakura
Thank you for your reply! However, I am working...

Thank you for your reply!
However, I am working on non-model organism, therefore, I do not have the annotation.
We have the genomic sequence (.fa file) but it is not available on UCSU or other...
Forum: Bioinformatics 11-12-2014, 09:48 PM
Replies: 4
Views: 1,208
Posted By angel-sakura
Smile How to extract gene_id from a specific locus?

Hello everyone,
I'm looking for updtream or downstream transciption factors and lncRNA of some specific genes. Just wandering is there any command or method that can extract gene_id from cuffdiff or...
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