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Forum: RNA Sequencing 05-19-2012, 11:11 PM
Replies: 47
Views: 43,284
Posted By natstreet
Cuffdiff zero FPKM with reference GFF

I have the exact same problem of having zero FPKM values for all genes that have a reference transcript. In my case, the GFF reference file comes from phytozome. I have run it through gffread to be...
Forum: Bioinformatics 02-15-2012, 09:39 PM
Replies: 5
Views: 2,861
Posted By natstreet
If you are mapping directly to a transcriptome I...

If you are mapping directly to a transcriptome I would maybe suggest trying RSEM and supplying it with a FASTA file of reference transcripts containing only one isoform per gene. The RSEM paper is...
Forum: Bioinformatics 01-09-2012, 04:20 AM
Replies: 6
Views: 2,991
Posted By natstreet
Your transcript contigs will contain many cases...

Your transcript contigs will contain many cases of spliced exons, including alternative splicing. How will you handle such cases if you throw both transcripts and genomic contigs into CAP3 together?
Forum: Bioinformatics 12-29-2011, 11:23 PM
Replies: 15
Views: 23,553
Posted By natstreet
I have understood the cuffdiff documentation the...

I have understood the cuffdiff documentation the same way - each comma separated list of files represent replicates (not necessarily technical) of a sample group.

To me, cummerbund is giving you...
Forum: Bioinformatics 11-13-2011, 08:39 PM
Replies: 1
Views: 1,697
Posted By natstreet
I have tried zorro on a genome of 450 MBp and I...

I have tried zorro on a genome of 450 MBp and I advise you not to try this. It is far too slow and basically unusable on a genome of this size.

I work on a project together with the developers of...
Forum: Bioinformatics 09-05-2011, 09:02 AM
Replies: 21
Views: 7,104
Posted By natstreet
Some time ago I used mosaik for a very similar...

Some time ago I used mosaik for a very similar task.
Forum: 454 Pyrosequencing 08-02-2011, 02:47 AM
Replies: 2
Views: 1,704
Posted By natstreet
I also have the same issue with v2.6. I'm finding...

I also have the same issue with v2.6. I'm finding that many assemblies that worked using v2.3 no longer work using 2.6. This is the case for cDNA and genomic assemblies. I've tried on Ubuntu and...
Forum: Bioinformatics 07-20-2011, 10:55 AM
Replies: 2
Views: 6,257
Posted By natstreet
I installed it in Ubuntu using the provided...

I installed it in Ubuntu using the provided setup.sh script by doing this

sudo ln -s /bin/true /bin/rocks
sudo ./setup.sh

It then seems to be working fine.
Forum: Bioinformatics 06-07-2011, 06:19 AM
Replies: 20
Views: 9,893
Posted By natstreet
Hi Seth Thanks for the pointer to...

Hi Seth

Thanks for the pointer to hapsembler, I hadn't come across it before. I'll test it out asap.
Forum: Bioinformatics 06-06-2011, 09:21 PM
Replies: 20
Views: 9,893
Posted By natstreet
Hi Seth How do you assess redundancy and how...

Hi Seth

How do you assess redundancy and how do you determine when two contigs are redundant and should be merged rather than being too different to each other? I'm not sure what species you work...
Forum: Bioinformatics 06-03-2011, 12:48 AM
Replies: 3
Views: 4,351
Posted By natstreet
I frequently use exonerate to align ESTs to a...

I frequently use exonerate to align ESTs to a genome using exonerate server. For example

fasta2esd genome.fasta genome.esd
esd2esi genome.esd genome.esi --memorylimit 2048

exonerate-server...
Forum: Bioinformatics 06-02-2011, 09:52 PM
Replies: 3
Views: 4,351
Posted By natstreet
I normally use exonerate...

I normally use exonerate (http://www.ebi.ac.uk/~guy/exonerate/) for this. Some alternative would include BLAT, sim4db (http://sourceforge.net/apps/mediawiki/kmer/index.php?title=Main_Page) and genome...
Forum: Bioinformatics 05-27-2011, 11:16 AM
Replies: 2
Views: 1,364
Posted By natstreet
I'm using fastaoverlap from exonerate...

I'm using fastaoverlap from exonerate (http://www.ebi.ac.uk/~guy/exonerate/) to do this.
Forum: Bioinformatics 05-26-2011, 10:44 PM
Replies: 4
Views: 4,145
Posted By natstreet
The download links at the address I posted will...

The download links at the address I posted will give you pre-compiled binaries.

Here are the commands I used

wget http://seq.cs.iastate.edu/CAP3/cap3.linux.i686_xeon64.tar

tar xf...
Forum: Bioinformatics 05-26-2011, 09:39 PM
Replies: 4
Views: 4,145
Posted By natstreet
All I did was download the 64bit version from...

All I did was download the 64bit version from here (http://seq.cs.iastate.edu/cap3.html). What have you tried, what doesn't work for you?
Forum: Bioinformatics 05-18-2011, 01:27 PM
Replies: 5
Views: 4,117
Posted By natstreet
I'm not sure what the relationship between var...

I'm not sure what the relationship between var and mean has to do with whether the samples are classified as biological or technical replicates. A biological replicate requires that the samples are...
Forum: Bioinformatics 05-18-2011, 02:30 AM
Replies: 5
Views: 4,117
Posted By natstreet
The answer to this shouldn't have anything to do...

The answer to this shouldn't have anything to do with DESeq - it's the same issue regardless of the software used. I would say the answer lies in part of your question

To me it is then clear -...
Forum: General 05-05-2011, 01:07 PM
Replies: 0
Views: 1,115
Posted By natstreet
TBLASTX 2.2.25 problem

I have performed the same search using tblastx 2.2.25 and 2.2.24. With 2.2.24 I get sensible hits but with the latest version I get no hits.

Does anyone know if something changed with the latest...
Forum: Bioinformatics 04-18-2011, 11:43 PM
Replies: 10
Views: 9,248
Posted By natstreet
Another option is the recently-released Zorro...

Another option is the recently-released Zorro (http://www.lge.ibi.unicamp.br/zorro/) (which is based on minimus2 but makes using NGS data friendlier). However, it is also for pairwise merging.
Forum: Bioinformatics 03-20-2011, 11:14 PM
Replies: 5
Views: 2,301
Posted By natstreet
As a good starting point I can recommend reading...

As a good starting point I can recommend reading through the posts at this (http://contig.wordpress.com/) blog. I think they will answer most of your questions but let us know if not.
Forum: Bioinformatics 03-18-2011, 12:04 AM
Replies: 2
Views: 3,532
Posted By natstreet
Can you show us the command you used to generate...

Can you show us the command you used to generate that value?
Forum: Bioinformatics 03-16-2011, 11:51 PM
Replies: 5
Views: 2,301
Posted By natstreet
Can you explain why you are not running a...

Can you explain why you are not running a transcript assembly and using isotigs as this would give you the information that you want.
Forum: Bioinformatics 02-21-2011, 10:44 PM
Replies: 34
Views: 17,367
Posted By natstreet
I can second (or third) the advice to check out...

I can second (or third) the advice to check out Galaxy. If you have someone fairly good with unix it's pretty easy to set up a local install, even if you work on an organism not included as a...
Forum: Bioinformatics 01-27-2011, 05:37 AM
Replies: 4
Views: 3,926
Posted By natstreet
same here...anyone spotted the solution/cause?

same here...anyone spotted the solution/cause?
Forum: Bioinformatics 01-24-2011, 01:08 AM
Replies: 12
Views: 6,958
Posted By natstreet
Can you give us some basic background about what...

Can you give us some basic background about what was sequenced - for example is it inbred or likely to be highly heterozygous? This will also affect your assembly results and different assemblers...
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