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Search: Posts Made By: adarob
Forum: Bioinformatics 05-21-2013, 02:47 PM
Replies: 38
Views: 11,168
Posted By adarob
Colons (":") cannot be used as separators in the...

Colons (":") cannot be used as separators in the reference names.
Forum: RNA Sequencing 12-10-2012, 10:46 AM
Replies: 67
Views: 71,825
Posted By adarob
sdriscoll, Note that in the case of a...

sdriscoll,

Note that in the case of a provided annotation, eXpress and Cufflinks use the same information to determine the transcript abundances. The spliced reads are no longer spliced in the...
Forum: Bioinformatics 11-19-2012, 06:31 PM
Replies: 0
Views: 984
Posted By adarob
eXpress manuscript now available!

Dear eXpress users,

We are pleased to announce that our manuscript on eXpress is now available on the Nature Methods website as an Advance Online Publication (direct link:...
Forum: Bioinformatics 11-13-2011, 01:39 PM
Replies: 17
Views: 6,782
Posted By adarob
A fix for this is being worked on and should be...

A fix for this is being worked on and should be released later this week. Sorry, but due to the overwhelming number of questions and reports, we are no longer able to respond to all e-mails at...
Forum: Bioinformatics 08-16-2011, 12:43 PM
Replies: 38
Views: 11,168
Posted By adarob
torfnase, can you send just the header to...

torfnase, can you send just the header to adarob@cs.berkeley.edu?
Forum: RNA Sequencing 05-17-2011, 03:16 PM
Replies: 38
Views: 17,194
Posted By adarob
There is a new utility included with cufflinks...

There is a new utility included with cufflinks now, called "gffread", which should be able to extract spliced transcript sequences from a GFF/GTF. This is now documented on this page (scroll down to...
Forum: RNA Sequencing 04-18-2011, 12:39 PM
Replies: 1
Views: 1,437
Posted By adarob
Yes. It should be the fasta file you mapped your...

Yes. It should be the fasta file you mapped your reads to.
Forum: RNA Sequencing 04-17-2011, 11:26 AM
Replies: 23
Views: 18,779
Posted By adarob
This type of bias (as well as sequence-specific...

This type of bias (as well as sequence-specific bias) is corrected for in Cufflinks. The importance of doing this correction is detailed in our paper here: http://genomebiology.com/2011/12/3/R22/
Forum: Bioinformatics 04-03-2011, 09:14 AM
Replies: 6
Views: 2,942
Posted By adarob
It looks like when you didn't provide an...

It looks like when you didn't provide an annotation, there was not enough available information to determine the fragment length distribution (see http://cufflinks.cbcb.umd.edu/howitworks.html#hdis)....
Forum: Bioinformatics 03-17-2011, 09:46 AM
Replies: 1
Views: 1,506
Posted By adarob
Cufflinks now corrects for library-specific...

Cufflinks now corrects for library-specific biases. The details, as well as examples of the different biases for different protocols (see the supplement) can be found in...
Forum: RNA Sequencing 02-02-2011, 03:17 PM
Replies: 25
Views: 6,070
Posted By adarob
I apologize for giving you inaccurate information...

I apologize for giving you inaccurate information earlier, but it turns out that my idea for making a pseudo-genome will not work unless your transcriptome is aligned so that you know which...
Forum: Bioinformatics 02-01-2011, 05:38 PM
Replies: 8
Views: 5,048
Posted By adarob
Can you paste the first few reads from both ends...

Can you paste the first few reads from both ends of the fastq files that are giving you problems?
Forum: Bioinformatics 01-31-2011, 11:08 AM
Replies: 8
Views: 5,048
Posted By adarob
Are you sure that all of your paired fastq files...

Are you sure that all of your paired fastq files have the same name for both reads?
Forum: Bioinformatics 01-26-2011, 03:50 PM
Replies: 1
Views: 1,407
Posted By adarob
This error is output by samtools (which Cufflinks...

This error is output by samtools (which Cufflinks calls) if you are using a SAM instead of a BAM. However, Cufflinks recognizes this and switches to SAM support, so there is no issue.

-Adam
Forum: Bioinformatics 01-24-2011, 12:32 PM
Replies: 35
Views: 10,631
Posted By adarob
fr-secondstrand See here:...

fr-secondstrand

See here: http://cufflinks.cbcb.umd.edu/manual.html#library
Forum: RNA Sequencing 01-05-2011, 09:26 PM
Replies: 25
Views: 6,070
Posted By adarob
I would look into RSEM if I were you.

I would look into RSEM if I were you.
Forum: RNA Sequencing 01-05-2011, 10:31 AM
Replies: 25
Views: 6,070
Posted By adarob
Yes, but it will probably be somewhat involved. ...

Yes, but it will probably be somewhat involved. You will need to build your GTF so that isoforms correctly overlap in the genome coordinates. You will then need to adjust your SAM alignments so...
Forum: RNA Sequencing 01-02-2011, 10:00 PM
Replies: 25
Views: 6,070
Posted By adarob
I just re-read your question, and it's not clear...

I just re-read your question, and it's not clear whether or not a reference genome is available. If it is, you can map your reads to the reference using your assembled transcriptome (GTF) as an...
Forum: RNA Sequencing 01-02-2011, 09:57 PM
Replies: 25
Views: 6,070
Posted By adarob
Cuffdiff is only meant for RNA-Seq analysis where...

Cuffdiff is only meant for RNA-Seq analysis where a reference genome is available. You can probably make it work for you by altering your alignment file to give your transcripts "dummy" genomic...
Forum: Bioinformatics 12-29-2010, 07:54 PM
Replies: 1
Views: 1,337
Posted By adarob
Exon information is all you need. You're good to...

Exon information is all you need. You're good to go!
Forum: Bioinformatics 12-25-2010, 10:55 AM
Replies: 11
Views: 6,593
Posted By adarob
@rgejman This issue has been resolved in...

@rgejman

This issue has been resolved in v0.9.3.
Forum: Bioinformatics 12-21-2010, 11:06 PM
Replies: 10
Views: 3,036
Posted By adarob
From Cole: Those are normal errors caused by...

From Cole:

Those are normal errors caused by too little data in complex genes. They get marked as FAIL in the expr and fpkm tracking files.

From Me:

You can try setting the min isoform...
Forum: Bioinformatics 12-12-2010, 05:53 PM
Replies: 3
Views: 1,930
Posted By adarob
Since they both are forced to use the same GTF in...

Since they both are forced to use the same GTF in cuffdiff, they will be on the same scale.
Forum: Bioinformatics 12-09-2010, 10:19 AM
Replies: 3
Views: 1,930
Posted By adarob
FPKM is Fragments Per Kilobase per Million reads...

FPKM is Fragments Per Kilobase per Million reads sequenced. Currently, Cufflinks calculates this "million reads sequenced" as "million reads mapped to the annotation", which is something we are...
Forum: RNA Sequencing 12-09-2010, 10:15 AM
Replies: 38
Views: 17,194
Posted By adarob
This software will do what you want. ...

This software will do what you want.

http://deweylab.biostat.wisc.edu/rsem/rsem-prepare-reference-bowtie.html
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