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Search: Posts Made By: cutcopy11
Forum: Bioinformatics 04-03-2013, 04:33 PM
Replies: 2
Views: 1,800
Posted By cutcopy11
Cannot find NOME-Seq data

Hello,

I am trying to find some NOME-Seq data, but I cannot locate it.

Here is the study ...

Genome Research 2012
"Genome-wide mapping of nucleosome positioning and DNA methylation within...
Forum: Bioinformatics 04-20-2012, 02:01 PM
Replies: 0
Views: 1,209
Posted By cutcopy11
quick basic questions about csfasta.ma.25.2 files

I am looking at some other people's processed data at GEO but I am unclear
about the alignment meanings.

Some information about *csfasta.ma files is found in the following guide:...
Forum: Bioinformatics 11-28-2011, 02:09 PM
Replies: 5
Views: 5,015
Posted By cutcopy11
Hi Simon, I may dig up my commands later,...

Hi Simon,

I may dig up my commands later, but I just wanted to say that when I said that DESeq reported around 7000 genes for the unfiltered estrogen dataset whereas edgeR reported around 500 to...
Forum: Bioinformatics 11-27-2011, 05:29 PM
Replies: 5
Views: 5,015
Posted By cutcopy11
The high number of differentially expressed genes...

The high number of differentially expressed genes in the 4 datasets may be due to the fact that I am essentially comparing apples and oranges.

The four datasets consist of either two different...
Forum: Bioinformatics 11-27-2011, 03:24 PM
Replies: 5
Views: 5,015
Posted By cutcopy11
Also, I would like to mention that the liver and...

Also, I would like to mention that the liver and kidney samples were derived from data
that was used in the EdgeR vignette.

I am not sure how their gene count data set was generated.

I used...
Forum: Bioinformatics 11-27-2011, 02:49 PM
Replies: 5
Views: 5,015
Posted By cutcopy11
DESeq and EdgeR: too many differentially expressed genes!?!?

Hello,

For a class project, I am mapping reads and counting reads per gene with RSEM for five different published RNA-seq datasets located at GEO / SRA. Most of the datasets were from raw RNA-seq...
Forum: Bioinformatics 11-27-2011, 07:37 AM
Replies: 36
Views: 17,786
Posted By cutcopy11
Hi Douglas, I appreciate your help but I...

Hi Douglas,

I appreciate your help but I cannot seem to figure out what might be a unique identifier that associate genes with rRNA within the GTF file. I have noticed, however, that the three...
Forum: Bioinformatics 11-26-2011, 08:32 PM
Replies: 36
Views: 17,786
Posted By cutcopy11
Thanks douglas for your quick response. Where do...

Thanks douglas for your quick response. Where do you recommend searching for those rRNA gene ids? Thanks again, Clay
Forum: Bioinformatics 11-26-2011, 06:15 PM
Replies: 36
Views: 17,786
Posted By cutcopy11
Hi DZhang and other SeqAnswer frequenters, I...

Hi DZhang and other SeqAnswer frequenters,

I want to filter rRNA and mtDNA genes from GTF files.

I am using RSEM to map and count reads per gene for a class project with RNA-seq data from from...
Forum: Bioinformatics 10-11-2011, 03:16 PM
Replies: 4
Views: 1,829
Posted By cutcopy11
I forgot to add --quality solexa64 but I still...

I forgot to add --quality solexa64 but I still could not get it to work


ckcollings@Anderson-Lab:~/Desktop/MYRNA_HOME$ ./myrna_local --input=./fastqfiles...
Forum: Bioinformatics 10-11-2011, 02:11 PM
Replies: 4
Views: 1,829
Posted By cutcopy11
Attempting to Perform MYRNA small example

Hello all,

I am trying to get MyRNA to work on an Ubuntu Linux platform.
Specifically, I could not get the small yeast example to work.

The SRA-tool-kit would not work as was a problem for...
Forum: Bioinformatics 10-05-2011, 02:33 PM
Replies: 6
Views: 2,681
Posted By cutcopy11
~/Desktop/MYRNA_HOME/example/yeast$...

~/Desktop/MYRNA_HOME/example/yeast$ ../../myrna_local --input=small.manifest --preprocess --reference=../../MYRNA_REFS/yeast_ensembl_61 --output=output_small --quality solexa64 --cpus=4

I got the...
Forum: Bioinformatics 06-23-2011, 11:03 AM
Replies: 1
Views: 2,159
Posted By cutcopy11
Bowtie Error Message

Hello,

I am trying to map some human reads with Bowtie, and after running the program, I received the message below and did not obtain statistics for mapping. It did apparently map 77.5 million...
Forum: Illumina/Solexa 08-11-2010, 12:12 AM
Replies: 19
Views: 6,107
Posted By cutcopy11
Is there a reliable target enrichment system...

Is there a reliable target enrichment system designed for SOLiD???
Forum: SOLiD 12-18-2009, 03:27 PM
Replies: 9
Views: 5,409
Posted By cutcopy11
Bowtie and Color Space

Hey, I tried the latest release of Bowtie, which now supports color space.

I downloaded the dataset from the link below and got the results further below after slightly less than 4 hours.

(I...
Forum: SOLiD 12-07-2009, 04:50 PM
Replies: 17
Views: 6,504
Posted By cutcopy11
Thanks for the quick response. After...

Thanks for the quick response.

After performing the "./configure" and "make" commands, the "make install" command gave the following output:

~/Desktop/bfast-0.6.1c$ make install
Making install...
Forum: SOLiD 12-07-2009, 02:33 PM
Replies: 17
Views: 6,504
Posted By cutcopy11
BFAST - Help

Hello,

I am trying to align Solid reads that map uniquely to the C. Elegans genome. I have a fastq file that has 4 lines for each read that are 50 bases in length. The reads are in color space...
Forum: Bioinformatics 11-10-2009, 06:56 PM
Replies: 2
Views: 1,409
Posted By cutcopy11
Thanks Ben

Thanks Ben
Forum: Bioinformatics 11-10-2009, 02:18 PM
Replies: 2
Views: 1,409
Posted By cutcopy11
Bowtie: ?'s about h_sapiens_37_asm index/outputs

Hello,

1)
I have a questions about bowtie's "h_sapiens_37_asm" index.
For the human genome, the concise reference sequences are numbered 0 to 24. I
assume these numbers represent chromosomes....
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