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Search: Posts Made By: cnyh
Forum: Bioinformatics 07-14-2013, 11:54 AM
Replies: 2
Views: 1,240
Posted By cnyh
Thanks! Will look into this.

Thanks! Will look into this.
Forum: Bioinformatics 07-14-2013, 02:35 AM
Replies: 2
Views: 1,240
Posted By cnyh
Extracting probe id's

I have downloaded some CEL files from GEO, and wish to annotate probe id's with AILUN. Can someone advise me about the most time-efficient way of extracting the probe id's from the CEL files? Is...
Forum: Bioinformatics 06-25-2013, 02:43 AM
Replies: 3
Views: 2,662
Posted By cnyh
IGV: empty tracks?

I am trying to load some .bam files into Integrated Genome Viewer. However, even when I zoom in to a particular gene that I've found to be differentially expressed in this data set, I don't see any...
Forum: Bioinformatics 05-13-2013, 10:39 AM
Replies: 11
Views: 1,836
Posted By cnyh
I am using the Ensembl GTF annotation, yes. I'm...

I am using the Ensembl GTF annotation, yes. I'm seeing four things in my GTF:
- gene_id
- gene_name
- transcript_id
- transcript_name

My question was primarily about ending up with the...
Forum: Bioinformatics 05-13-2013, 10:07 AM
Replies: 11
Views: 1,836
Posted By cnyh
Ah! I just recently ran the pipeline with the...

Ah! I just recently ran the pipeline with the Ensembl files, so I will try that approach and see whether it goes better. Thanks for the tip :)

Would you recommend using gene IDs or switching to...
Forum: Bioinformatics 05-13-2013, 05:20 AM
Replies: 11
Views: 1,836
Posted By cnyh
> head(error.fewerthanone) [1] "uc001aab.3"...

> head(error.fewerthanone)
[1] "uc001aab.3" "uc001aac.3" "uc001aae.3" "uc001aah.3" "uc001aak.2"
[6] "uc001aam.3"
Forum: Bioinformatics 05-13-2013, 05:20 AM
Replies: 11
Views: 1,836
Posted By cnyh
# Load libraries and files library(cummeRbund) ...

# Load libraries and files
library(cummeRbund)
cuff <- readCufflinks()
gene.individual <- fpkmMatrix(genes(cuff))
annotation <-...
Forum: Bioinformatics 05-13-2013, 05:09 AM
Replies: 11
Views: 1,836
Posted By cnyh
What we are looking for is a list of genes that...

What we are looking for is a list of genes that are differentially expressed between different organ metastases. The plan is to go on with biological validation of this gene list using knockout...
Forum: Bioinformatics 05-11-2013, 09:48 AM
Replies: 11
Views: 1,836
Posted By cnyh
Thank you. It is indeed for downstream analysis...

Thank you. It is indeed for downstream analysis that I need it (I just assumed it had to be tophat/bowtie that extracted information from the gtf, since I don't provide it to cuffdiff). However, my...
Forum: Bioinformatics 05-11-2013, 12:12 AM
Replies: 11
Views: 1,836
Posted By cnyh
Tophat/Bowtie not using gene symbols from gtf file

I have supplied Tophat/Bowtie with a gtf file from Ensembl. However, instead of making use of the gene symbols (the column "gene_name" in the gtf file, for example "DDX11L1"), it seems to use the...
Forum: Bioinformatics 05-04-2013, 04:52 AM
Replies: 1
Views: 2,017
Posted By cnyh
Converting chromosome names in gtf file

The TopHat manual tells me that "the values in the first column of the provided GTF/GFF file [...] must match the name of the reference sequence in the Bowtie index you are using with TopHat."

I...
Forum: RNA Sequencing 04-24-2013, 01:40 AM
Replies: 10
Views: 5,733
Posted By cnyh
That's what I understand, but I'm no expert in...

That's what I understand, but I'm no expert in this.
Forum: RNA Sequencing 04-24-2013, 12:15 AM
Replies: 10
Views: 5,733
Posted By cnyh
The reason for that is that cuffdiff additionally...

The reason for that is that cuffdiff additionally normalizes the counts values.
Forum: Bioinformatics 03-08-2013, 10:00 AM
Replies: 2
Views: 1,879
Posted By cnyh
Ah, I see. So alpha is the cutoff for the p-value...

Ah, I see. So alpha is the cutoff for the p-value then. Does the same apply for q-value as well?
Forum: Bioinformatics 03-08-2013, 09:59 AM
Replies: 4
Views: 1,212
Posted By cnyh
Yes! Great, that does look like what I'm looking...

Yes! Great, that does look like what I'm looking for. Thanks :)
Forum: Introductions 03-08-2013, 08:30 AM
Replies: 0
Views: 648
Posted By cnyh
Bazinga!

It took me a few tries, but I finally found a title that failed to find similar threads :)

I think the whole idea of a community answering each other's questions in this manner is a wonderful...
Forum: Bioinformatics 03-08-2013, 08:22 AM
Replies: 2
Views: 1,879
Posted By cnyh
cummeRbund getSig(): alpha?

I've used the following command to extract significant genes:

mySigGenes <- getSig(cuff, alpha = 0.05, level = "genes")

However, I don't understand why terms familiar to me such as "FPKM" and...
Forum: Bioinformatics 03-08-2013, 08:21 AM
Replies: 1
Views: 1,218
Posted By cnyh
How do I find read depth?

With Illumina RNA-Seq data that I've analyzed via TopHat/Bowtie and cufflinks/cuffdiff, what command can I use to find out what the read depth of my samples is?
Forum: Bioinformatics 03-08-2013, 08:18 AM
Replies: 4
Views: 1,212
Posted By cnyh
Thank you. I just understood after reading...

Thank you. I just understood after reading through that response and doing a bit of googling that I've been using the wrong term. Apparently it's not "Entrez Gene ID" I am looking for, but "Approved...
Forum: Bioinformatics 03-08-2013, 07:49 AM
Replies: 4
Views: 1,212
Posted By cnyh
Annotate diff files

Perhaps this is a better place to ask this question:

I've run cuffdiff on my RNA-Seq data using UCSC_Genes.gtf as my transcript reference, and looked at the file gene_exp.diff. Here I see that the...
Forum: RNA Sequencing 03-06-2013, 05:17 AM
Replies: 3
Views: 1,604
Posted By cnyh
That does look very helpful indeed. Thanks for...

That does look very helpful indeed. Thanks for the tip!
Forum: RNA Sequencing 03-06-2013, 05:00 AM
Replies: 10
Views: 5,733
Posted By cnyh
I see. And I assume by that one can avoid the...

I see. And I assume by that one can avoid the stringency issues that cuffdiff has with calculating q-values? That would be very promising. Thank you very much.

In that case I have a related...
Forum: RNA Sequencing 03-06-2013, 04:59 AM
Replies: 3
Views: 1,604
Posted By cnyh
GTF file with one line per gene?

I would like to use bedtools to extract raw gene counts from my .bam files. However, I was using UCSC_Genes.gtf (human) as my source file, but that file contains multiple lines for each gene, which...
Forum: RNA Sequencing 03-06-2013, 04:41 AM
Replies: 10
Views: 5,733
Posted By cnyh
Thank you for your quick response! - It is...

Thank you for your quick response!
- It is indeed differential expression between different samples that we are interested in.
- We have primarily been using cuffdiff for the purposes of DE.
...
Forum: RNA Sequencing 03-06-2013, 04:32 AM
Replies: 0
Views: 984
Posted By cnyh
Annotate diff files

I've run cuffdiff on my RNA-Seq data using UCSC_Genes.gtf as my transcript reference, and looked at the file gene_exp.diff. Here I see that the columns test_id and gene_id are both based on UCSC gene...
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