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Forum: De novo discovery 02-28-2012, 10:44 AM
Replies: 82
Views: 42,130
Posted By Marta
Hi edge, No sure what you are referring to...

Hi edge,

No sure what you are referring to in "Fail to get main class". You'll need to contact the support of the program you are using. If this is from CLC bio trial, write to...
Forum: De novo discovery 02-27-2012, 09:14 PM
Replies: 82
Views: 42,130
Posted By Marta
Hi Edge, you may want to try the following: ...

Hi Edge,

you may want to try the following:

1. save the contigs created by each assembler in .fasta format. Or save just 1000 (or 100) longest contigs
2. download RefSeq proteins of your...
Forum: De novo discovery 02-27-2012, 08:22 PM
Replies: 82
Views: 42,130
Posted By Marta
How about BLASTX against RefSeq of related...

How about BLASTX against RefSeq of related species or group? I always wanted to see uninterrupted ORFs of expected size. I also always check for the presence of the longest transcript expected in...
Forum: Events / Conferences 01-07-2010, 01:52 PM
Replies: 5
Views: 3,681
Posted By Marta
I realized after posting that this thread is over...

I realized after posting that this thread is over a year old!
Forum: Events / Conferences 01-07-2010, 01:48 PM
Replies: 5
Views: 3,681
Posted By Marta
I will be there with a poster (#14) and two...

I will be there with a poster (#14) and two talks.

Marta
Forum: De novo discovery 12-16-2009, 10:22 PM
Replies: 82
Views: 42,130
Posted By Marta
The experiment CLC did for this white paper does...

The experiment CLC did for this white paper does not reflect the actual performance of the CLC assembler. I think the assembler is much better than what the paper claims.

I use CLC Genomics...
Forum: De novo discovery 12-16-2009, 11:02 AM
Replies: 82
Views: 42,130
Posted By Marta
KevinLam, The data is unpublished. We are...

KevinLam,

The data is unpublished. We are re-assembling the reads using the latest version of CLC assembler and Velvet with adjusted parameters. The number of transcriptome contigs in our latest...
Forum: De novo discovery 12-02-2009, 07:36 AM
Replies: 82
Views: 42,130
Posted By Marta
We assembled lettuce transcriptome using 85 nt...

We assembled lettuce transcriptome using 85 nt IGA single reads. We used CLC and Velvet followed by CAP3.
Forum: Sample Prep / Library Generation 11-28-2009, 05:34 PM
Replies: 4
Views: 3,181
Posted By Marta
I tested NEB Fragmentase for generation of long...

I tested NEB Fragmentase for generation of long DNA fragments: (http://www.genomecenter.ucdavis.edu/dna_technologies/documents/fragmentase_large_frag_protocol.pdf )

Marta
Forum: Sample Prep / Library Generation 11-23-2009, 10:00 AM
Replies: 7
Views: 9,602
Posted By Marta
I use 2% agarose in TBE with GelRed followed by...

I use 2% agarose in TBE with GelRed followed by fragment extraction using NucleoTrap from Macherey-Nagel (or Clontech). I did not see any problems with 50C incubation for agarose melting step in...
Forum: General 11-19-2009, 07:46 AM
Replies: 14
Views: 13,455
Posted By Marta
Thanks again simonandrews

Thanks again simonandrews
Forum: General 11-18-2009, 11:03 AM
Replies: 14
Views: 13,455
Posted By Marta
simonandrews, Thank you very much for your...

simonandrews,

Thank you very much for your posting. I did not experienced/realized this problem yet - the only way I used the indexes is by combining 12 libraries into one pool. In future I may...
Forum: General 11-17-2009, 07:28 AM
Replies: 14
Views: 13,455
Posted By Marta
I did not see any problems with analysis of...

I did not see any problems with analysis of unbalanced base composition. The main problem with pooling I experienced is unequal amounts of reads from different libraries in the pool. This is not...
Forum: Bioinformatics 11-17-2009, 06:26 AM
Replies: 236
Views: 503,884
Posted By Marta
Stegger, thanks! Is is nice to know that CLC...

Stegger, thanks! Is is nice to know that CLC Workbench can run on a 3GB machine. How long are your 10M reads?
Forum: Bioinformatics 11-16-2009, 09:38 PM
Replies: 236
Views: 503,884
Posted By Marta
Yes, CLC Genomics Workbench will use all three...

Yes, CLC Genomics Workbench will use all three data types. I use the program on Windows. However you will need lots of RAM. For my files/genomes I needed 32GB (the max we could put into my box). ...
Forum: General 11-16-2009, 09:20 PM
Replies: 14
Views: 13,455
Posted By Marta
I developed PE indexed adapters for our needs. ...

I developed PE indexed adapters for our needs. They worked fine w/o any special modifications, just 5'-P for all PE-1 adapters. We read the index as first 6 letters in each direction. The file can...
Forum: Illumina/Solexa 10-23-2009, 11:35 AM
Replies: 19
Views: 11,004
Posted By Marta
The new v1.5 small RNA prep protocol seems to be...

The new v1.5 small RNA prep protocol seems to be working fine for me. I just finished analysis where I compared how many tags from the specific gene, and from tRNAs, rRNAs, and chloroplasts we got...
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