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Search: Posts Made By: marcora
Forum: Bioinformatics 04-15-2013, 07:34 AM
Replies: 23
Views: 26,294
Posted By marcora
The command that you referenced is for genome...

The command that you referenced is for genome annotation files from ENSEMBL (release 60), not for UCSC files.
Forum: Bioinformatics 03-30-2012, 12:27 PM
Replies: 21
Views: 10,656
Posted By marcora
The best I could find is in here...

The best I could find is in here http://bioserver.hci.utah.edu/TestDatasets/
Forum: Bioinformatics 04-18-2011, 02:06 AM
Replies: 21
Views: 10,656
Posted By marcora
I was thinking more in the line of a tool that...

I was thinking more in the line of a tool that can generate a transcriptome of known composition (with, e.g., 100 defined genes differentially expressed at various levels), and then simulate the...
Forum: Bioinformatics 04-18-2011, 02:01 AM
Replies: 21
Views: 10,656
Posted By marcora
Thumbs up Got it! Thanx a lot for your valuable help.

Got it! Thanx a lot for your valuable help.
Forum: Bioinformatics 04-18-2011, 01:45 AM
Replies: 21
Views: 10,656
Posted By marcora
Smile Have you read this...

Have you read this http://cufflinks.cbcb.umd.edu/howitworks.html#hdif, I did but I cannot quite understand it (I am not a biostatistician).

Going back to the original question... do you know of...
Forum: Bioinformatics 04-18-2011, 12:27 AM
Replies: 21
Views: 10,656
Posted By marcora
Dear Simon, thank you for your answer. I...

Dear Simon,

thank you for your answer. I really appreciate your contributions to this forum, which make bench biologists like me understand better the statistical ground of the tools we use for...
Forum: Bioinformatics 04-17-2011, 08:49 AM
Replies: 2
Views: 1,466
Posted By marcora
Simon Anders wrote very good documentation for...

Simon Anders wrote very good documentation for DESeq, which you can read HERE (http://www.bioconductor.org/packages//release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf) (the format of the input file is...
Forum: Bioinformatics 04-16-2011, 02:36 AM
Replies: 21
Views: 10,656
Posted By marcora
Unhappy Testing/benchmarking RNASeq DE tools

I am performing DE analysis of RNAseq datasets using DESeq, edgeR, and CuffDiff. While DESeq and edger (based on very similar models) agree for the most part, I have found that CuffDiff gives very...
Forum: Bioinformatics 04-16-2011, 01:24 AM
Replies: 16
Views: 5,207
Posted By marcora
Has anybody been successful in generating a...

Has anybody been successful in generating a synthetic "truth dataset" for RNAseq. I am comparing cuffdiff to deseq and I am getting very different results. Which one should I pick? I can't answer...
Forum: Bioinformatics 04-10-2011, 10:44 PM
Replies: 52
Views: 75,445
Posted By marcora
If I was a reviewer I would doubt any conclusion...

If I was a reviewer I would doubt any conclusion coming from an experiment with no biological replicates. Anyhow, DESeq allows for such design, you may wanna consider it. I am not familiar with CLC...
Forum: Bioinformatics 02-16-2011, 01:42 AM
Replies: 13
Views: 5,999
Posted By marcora
You don't need cufflinks/cuffcompare output to...

You don't need cufflinks/cuffcompare output to calculate the raw read counts, just tophat (or another read mapper) output and an annotation file (containing the features you want to apply the count...
Forum: Bioinformatics 01-14-2011, 02:11 AM
Replies: 191
Views: 57,844
Posted By marcora
Here we go! ;)

Here we go! ;)
Forum: Bioinformatics 01-12-2011, 02:47 AM
Replies: 5
Views: 1,929
Posted By marcora
I would recommend at least 4 Gb of RAM and a...

I would recommend at least 4 Gb of RAM and a multiprocessor CPU (like Intel i7). I have been doing all of my work with such a machine (using Ubuntu Linux 64 bit) w/o any major problem.

Hope this...
Forum: Bioinformatics 01-11-2011, 07:56 AM
Replies: 13
Views: 5,999
Posted By marcora
Smile You are correct. I use the transcripts.gtf files...

You are correct. I use the transcripts.gtf files (only one of them really, since I don't do de-novo transcript discovery but only use a reference annotation) from cufflinks to generate a...
Forum: Bioinformatics 01-11-2011, 02:06 AM
Replies: 13
Views: 5,999
Posted By marcora
Cool The only tool where you can input replicates is...

The only tool where you can input replicates is cuffdiff. I use the following bash script to run it (but it is build based on my personal convention of naming and organizing the input files). In...
Forum: Bioinformatics 01-10-2011, 04:02 AM
Replies: 15
Views: 5,745
Posted By marcora
Smile After much struggling and with the help of a...

After much struggling and with the help of a member of this forum I have finally been able to use Ensembl GTF files with TopHat.

Please find a detailed answer to your problem here...
Forum: Bioinformatics 01-10-2011, 02:39 AM
Replies: 191
Views: 57,844
Posted By marcora
Cool Hi Simon, is BAM support in HTSeq coming...

Hi Simon,

is BAM support in HTSeq coming soon!?!

Keep up the good work! :)
Forum: Bioinformatics 01-06-2011, 09:22 AM
Replies: 23
Views: 26,294
Posted By marcora
Talking My bad! This last time when I ran tophat I didn't...

My bad! This last time when I ran tophat I didn't rename the cleaned GTF file to "mm9.ensembl" and therefore tophat couldn't find it. Surprisingly, instead of reporting a missing file, tophat gave me...
Forum: Bioinformatics 01-06-2011, 09:05 AM
Replies: 23
Views: 26,294
Posted By marcora
#!/bin/bash GENOME=mm9 GENES=mm9.ensembl ...

#!/bin/bash

GENOME=mm9
GENES=mm9.ensembl

for f in $( ls *.fq ); do
if [ -f $f ]; then
mkdir $f.tophat
tophat -p 8 --library-type fr-unstranded --solexa1.3-quals -G...
Forum: Bioinformatics 01-06-2011, 08:59 AM
Replies: 23
Views: 26,294
Posted By marcora
Unhappy First and foremost, thank you for your help and...

First and foremost, thank you for your help and patience.

I removed the offending lines as you indicated and now my GTF file passes the gtf_juncs test without warnings or errors.

However,...
Forum: Bioinformatics 01-06-2011, 07:37 AM
Replies: 23
Views: 26,294
Posted By marcora
Unhappy I tried one more thing: 1) I loaded the...

I tried one more thing:

1) I loaded the awk-modified GTF file as a custom track into the UCSC genome browser against NCBI37/mm9. The browser complained about annotations starting with chrNT and...
Forum: Bioinformatics 01-06-2011, 06:37 AM
Replies: 23
Views: 26,294
Posted By marcora
Red face I have already tried that before, but just in...

I have already tried that before, but just in case I re-tried today.

1) I downloaded the latest gtf file for mus musculus from ftp://ftp.ensembl.org/pub/current/gtf/

2) I ran your awk one-liner...
Forum: Bioinformatics 01-05-2011, 09:21 AM
Replies: 23
Views: 26,294
Posted By marcora
I don't quite understand yet why (even with the...

I don't quite understand yet why (even with the correct naming of chromosomes etc in the bowtie index) tophat and cufflinks only seem to work with refFlat against mm9, instead of with any well-formed...
Forum: Bioinformatics 01-04-2011, 02:44 PM
Replies: 2
Views: 1,175
Posted By marcora
FastQC...

FastQC (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) also runs a check for duplication and report the total duplication value with a warning if too high!
Forum: Bioinformatics 12-22-2010, 09:18 PM
Replies: 13
Views: 5,999
Posted By marcora
As a test, I ran cuffdiff and deseq comparing,...

As a test, I ran cuffdiff and deseq comparing, e.g., cortical tissue to cortical tissue (instead of cortical tissue to striatal tissue like in the aforementioned experiment). Interestingly, deseq is...
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