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Forum: Bioinformatics 10-09-2014, 05:46 AM
Replies: 1
Views: 4,123
Posted By hchang10
I noticed this too. If anyone could explain the...

I noticed this too. If anyone could explain the differences between XLOC (gene id) and TCONS (transcript id), I'll really appreciate.
Forum: RNA Sequencing 08-22-2014, 12:27 PM
Replies: 1
Views: 1,830
Posted By hchang10
edgeR for unequal replicated samples

Hi folks,

I have a question about how to do DE analysis of an unequal replicated RNA-Seq data? The design looks like:

Treatment 5day 7day 9day
A 1rep ...
Forum: Bioinformatics 06-23-2013, 02:01 AM
Replies: 0
Views: 3,853
Posted By hchang10
PCA vs MDS plots

Hi guys,

I'm confusing about how is the difference between principle component plot (PCA) and multi-dimension scaling plot (MDS). I have six RNA-Seq samples with three replications for two...
Forum: Bioinformatics 06-17-2013, 05:51 PM
Replies: 0
Views: 1,316
Posted By hchang10
gffread option

Hi everyone,

I'd like to convert gtf file to fasta file by gffread. However, the output gave me the header in transcript_id, like ">TCONS_00000568 gene=XLOC_000524". Is there anyway I could...
Forum: Bioinformatics 06-13-2013, 08:34 AM
Replies: 4
Views: 6,729
Posted By hchang10
Awesome!!! Dario, I appreciate it!!!! ...

Awesome!!!

Dario, I appreciate it!!!!

Thank you so much!!!!
Forum: Bioinformatics 06-12-2013, 09:44 AM
Replies: 4
Views: 6,729
Posted By hchang10
Filter multi-fasta by length

Hi everyone,

I'd like to filter a multi-fasta file by length, for example, keep length <300bp and filter out longer ones. I knew there is tool in Galaxy doing this, but it takes so long to...
Forum: Bioinformatics 05-30-2013, 07:53 PM
Replies: 26
Views: 3,741
Posted By hchang10
Thank you chadn737~ (Then I guess you're a...

Thank you chadn737~ (Then I guess you're a professor somewhere!)

I just asked another friend, and she said it depends. I have asked her to send me a paper which only did one replication but...
Forum: Bioinformatics 05-30-2013, 07:44 PM
Replies: 26
Views: 3,741
Posted By hchang10
Thank you guys~ Dear chadn737, I meant three...

Thank you guys~

Dear chadn737, I meant three samples and extracting RNA from them for library construction.

Like:

control Rep1, Rep2, Rep3 >>> RNA1, RNA2, RNA3 >>>library1, library2,...
Forum: Bioinformatics 05-30-2013, 07:12 PM
Replies: 26
Views: 3,741
Posted By hchang10
Does NGS need replication?

Hi Guys,

I have a friend told me that NGS does not need replication. In his experiment, he only submit two sample library, control and treatment. That's all. Is this correct?

In my case,...
Forum: RNA Sequencing 05-30-2013, 11:35 AM
Replies: 0
Views: 961
Posted By hchang10
How to separate significant genes in Cuffdiff output?

Hi Everyone,

I have a question about how to separate the significant differential expressed gene in Cuffdiff output. I tried to use Excel, and sort by yes/no column, but the save format messed...
Forum: RNA Sequencing 05-25-2013, 12:50 PM
Replies: 0
Views: 963
Posted By hchang10
The Transcript Length from Cufflinks

Hi Guys,

I'm doing a fungus RNA-Seq.However, the merged transcriptome gave me very long transcripts (generally >2K). I used GeneMarES to do some sampling prediction, and found cases that...
Forum: RNA Sequencing 05-15-2013, 07:40 PM
Replies: 4
Views: 1,389
Posted By hchang10
Thank you for responding. The problem is, I...

Thank you for responding.

The problem is, I found more than one genes in a Cufflinks-predicted transcript. So my friend raised the doubts whether the assembly Cufflinks did is good or not. Does it...
Forum: RNA Sequencing 05-14-2013, 01:25 PM
Replies: 4
Views: 1,389
Posted By hchang10
Does Cufflinks Give Me Trascriptomes?

Hi Everyone,

I'm a beginner in this area, please forget any silly question.

My situation is that I have a raw scaffold whole genome sequences for my organism, but not annotated at all....
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