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Forum: RNA Sequencing 06-27-2017, 06:11 PM
Replies: 0
Views: 1,023
Posted By tigerxu
How to extract the circRNA sequences based on the the back-spliced junctions detected

Dear All,

I have used several tools (findcirc, Circexplorer, DCC) to detect the circRNAs from mouse tissue. I have generated a list containing back-spliced junctions for each circRNA detected. An...
Forum: RNA Sequencing 10-10-2014, 10:20 AM
Replies: 7
Views: 2,477
Posted By tigerxu
Many thanks for your help! I will use your script...

Many thanks for your help! I will use your script on my data.
Forum: Epigenetics 09-26-2014, 04:32 AM
Replies: 31
Views: 31,183
Posted By tigerxu
Thanks a lot for your quick and useful reply,...

Thanks a lot for your quick and useful reply, Felix!
Forum: Epigenetics 09-26-2014, 03:16 AM
Replies: 31
Views: 31,183
Posted By tigerxu
Hi Felix, Can I ask you a question? I plan to...

Hi Felix, Can I ask you a question? I plan to start a RRBS sequencing but I don't know if I should choose single-end or paired-end sequencing. Would you like to give me advice which one is better...
Forum: RNA Sequencing 09-16-2014, 10:30 AM
Replies: 0
Views: 1,019
Posted By tigerxu
Extract a gene list from a gtf file produced by Cuffmerge

I have a gtf file produced by Cuffmerge. The reference genome I used is UCSC mm10. According to the manual of cufflinks, the new genes are represented by class_code "u".

I want to add a cutoff...
Forum: Bioinformatics 07-17-2014, 12:49 PM
Replies: 92
Views: 36,192
Posted By tigerxu
I very appreciate your information! Very helpful...

I very appreciate your information! Very helpful to further my understanding on the statistical background of GAGE.
Forum: RNA Sequencing 07-17-2014, 04:34 AM
Replies: 7
Views: 2,477
Posted By tigerxu
Thanks very much for your advices, syfo and...

Thanks very much for your advices, syfo and blancha! I will notice these points.
Forum: RNA Sequencing 07-15-2014, 10:23 AM
Replies: 7
Views: 2,477
Posted By tigerxu
Thanks! Their paper didn't mention the...

Thanks! Their paper didn't mention the tools/pipeline to identify long ncRNA from RNA-seq data. I will ask them if possible.
Forum: RNA Sequencing 07-14-2014, 03:12 AM
Replies: 7
Views: 2,477
Posted By tigerxu
Software for prediction of long non-coding RNAs from RNA-seq data

I want to detect novel long non-coding RNAs from the mammalian RNA-seq data. Can you recommend some excellent tools for this analyses aim?

Thanks!
Forum: Bioinformatics 07-11-2014, 12:26 PM
Replies: 92
Views: 36,192
Posted By tigerxu
I have followed the default workflows of gage and...

I have followed the default workflows of gage and pathview on the example RNA-seq dataset. I also used the fold changes inferred by deseq2, then followed by the gage and pathview. I found both...
Forum: Bioinformatics 07-10-2014, 06:26 AM
Replies: 92
Views: 36,192
Posted By tigerxu
Okay, thank! I will try version 2.14.3 later.

Okay, thank! I will try version 2.14.3 later.
Forum: Bioinformatics 07-09-2014, 10:39 AM
Replies: 92
Views: 36,192
Posted By tigerxu
The problem is still there. But I have modified...

The problem is still there. But I have modified the margins parameters in the internal function sigGeneSet within the gage package. It can work!
Forum: Bioinformatics 07-09-2014, 03:06 AM
Replies: 92
Views: 36,192
Posted By tigerxu
other attached packages: [1] gage_2.14.2 ...

other attached packages:
[1] gage_2.14.2 GenomicAlignments_1.0.2
[3] BSgenome_1.32.0 Rsamtools_1.16.1
[5] Biostrings_2.32.0 XVector_0.4.0 ...
Forum: Bioinformatics 07-07-2014, 03:13 AM
Replies: 92
Views: 36,192
Posted By tigerxu
I have a question about the margin argument in...

I have a question about the margin argument in the sigGeneSet function when I run the following command
> rcount.kegg.sig<-sigGeneSet(rcount.kegg.p, outname="sig.kegg",pdf.size=c(7,12),margins=c(5,...
Forum: RNA Sequencing 06-13-2014, 10:26 AM
Replies: 2
Views: 3,338
Posted By tigerxu
Many thanks for your advice! I got it.

Many thanks for your advice! I got it.
Forum: RNA Sequencing 06-10-2014, 06:39 AM
Replies: 2
Views: 3,338
Posted By tigerxu
Length interval of long non-coding RNAs?

According to some references, long non-coding RNAs (lncRNAs) is composed of non-coding RNAs (ncRNAs) with long transcript length (>200 nt).

I'm wondering how I can know the length distribution of...
Forum: Academic/Non-Profit Jobs 02-10-2014, 05:49 AM
Replies: 3
Views: 940
Posted By tigerxu
Can you tell me if you are going to employ a...

Can you tell me if you are going to employ a bioinformatician with master degree or PhD degree? Thanks!
Forum: Metagenomics 10-17-2013, 04:03 AM
Replies: 4
Views: 1,807
Posted By tigerxu
Sure, I will try MG-RAST. Thanks!

Sure, I will try MG-RAST. Thanks!
Forum: Metagenomics 10-17-2013, 03:53 AM
Replies: 4
Views: 1,807
Posted By tigerxu
Thank you rhinoceros! I forgot a point. I...

Thank you rhinoceros!

I forgot a point. I hope to find a standalone software not web-based server. As MG-RAST or IMG is sometimes long waiting. I'm wondering if there is other fast and local...
Forum: Metagenomics 10-17-2013, 01:22 AM
Replies: 4
Views: 1,807
Posted By tigerxu
Best approach to analyze taxonomic profiling of metagenomes from environmental sample

I'm wondering which tool currently available is best for analyzing taxonomic profiling of environmental microbial community (non-human microbiome), e.g. soil, marine, sediment? I suppose that the...
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