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Forum: RNA Sequencing 01-12-2017, 09:21 AM
Replies: 0
Views: 1,141
Posted By anth
Optimal insert size for de novo assembly from PE150 reads

In the past, I have had reasonable success with de novo assembly of non-model eukaryotes with insert sizes of ~300 bp, using 100 bp PE and Trinity for assembly.

With 150 bp PE reads and the...
Forum: Bioinformatics 09-17-2014, 11:44 AM
Replies: 0
Views: 1,751
Posted By anth
GO enrichment analysis for a non-model system

I have data from a few RNAseq experiments on a non-model eukaryote, in which I have assembled transcriptomes with Trinity and analyzed expression with EdgeR (after mapping back to the transcriptome)....
Forum: Bioinformatics 08-25-2014, 02:26 PM
Replies: 0
Views: 1,122
Posted By anth
Unexpected SOAPdenovo2 behavior - contigs conflict with scaffolds

We are presently working on the sequencing and assembly of a draft genome of a ~1 Gb invertebrate. The preliminary dataset is a HiSeq single lane of PE100, with a 300 bp insert size. Larger insert...
Forum: Bioinformatics 06-30-2014, 07:37 AM
Replies: 4
Views: 2,672
Posted By anth
Thanks! It worked. I hope that Trinotate and...

Thanks! It worked. I hope that Trinotate and TrinotateWeb continue to develop!

What have you done for downstream GO enrichment tests and pathway mapping, using Trinotate?
Forum: Bioinformatics 06-27-2014, 02:26 PM
Replies: 0
Views: 1,162
Posted By anth
Mapping transcripts to Kegg gene IDs / Using Paintomics on a non-Kegg species

I would like to use Paintomics on a species not present in the Kegg database. Our work is on congeners of a species which is presently included in Paintomics. What is the best way to map my...
Forum: Bioinformatics 06-13-2014, 11:39 AM
Replies: 4
Views: 2,672
Posted By anth
TrinotateWeb confusion: Populating Trinotate.sqlite with Expression Data

I have run TrinotateWeb with the test data (and can view via the web interface and all), but I am confused by the usage with my own data.

Specifically, when I Populate Trinotate.sqlite with...
Forum: Metagenomics 05-13-2014, 02:28 PM
Replies: 7
Views: 4,467
Posted By anth
Wow, thanks for all of the helpful replies! ...

Wow, thanks for all of the helpful replies!

I have one further question - some of our samples are quite low concentration (as low as 10 ng/ul, in 50 ul (total of 0.5 ug). What would be the best...
Forum: Metagenomics 05-12-2014, 03:06 PM
Replies: 7
Views: 4,467
Posted By anth
Thanks for your replies. As for aims, the primary...

Thanks for your replies. As for aims, the primary interest is in gene inventory / genomic potential, and we would be thrilled to be able to make a reasonable draft assembly of the two most common...
Forum: Metagenomics 04-30-2014, 12:51 PM
Replies: 7
Views: 4,467
Posted By anth
Considerations for a pilot study: HiSeq SR100 vs. MiSeq PE300

I am involved in a pilot experiment to examine the metagenomes of two environmental samples. This is largely exploratory at this point, with the intent being cataloging the genomic potential of the...
Forum: Bioinformatics 11-17-2013, 12:47 PM
Replies: 3
Views: 990
Posted By anth
Why not perform a de novo assembly with your...

Why not perform a de novo assembly with your RNAseq data instead?
Forum: Bioinformatics 10-23-2013, 01:34 PM
Replies: 24
Views: 9,066
Posted By anth
Thank you for your concern. The machine will be...

Thank you for your concern. The machine will be administered by (and located in) our IT department. I was presented with options by our IT department, but they are not computational biologists, and...
Forum: Bioinformatics 10-22-2013, 06:26 PM
Replies: 24
Views: 9,066
Posted By anth
Hello again, I have yet another...

Hello again,

I have yet another consideration. Looking at various configurations, the lower price of the AMD Opteron CPUs quickly becomes apparent, in comparison to Xeon 2600v2 and 4600 CPUs.
...
Forum: Bioinformatics 10-20-2013, 08:22 AM
Replies: 24
Views: 9,066
Posted By anth
Thanks for your input, Wallysb01. I will...

Thanks for your input, Wallysb01. I will certainly not go with RAID5. Actually, the colleague's machine I have been using has both a RAID1 and RAID0 array as you describe, and it has worked nicely...
Forum: Bioinformatics 10-19-2013, 10:37 AM
Replies: 24
Views: 9,066
Posted By anth
Thank you for all of the responses. I truly...

Thank you for all of the responses. I truly appreciate it.

One of the other options we had considered was going with a pair of Intel Xeon E5-2650v2 2.6GHz CPUs. However, in the end, the price...
Forum: Bioinformatics 10-17-2013, 05:31 PM
Replies: 24
Views: 9,066
Posted By anth
Question Hardware for de novo assembly of 1 Gb genomes

I recently started work in a lab where I have a budget of approximately $20,000 to spend on a workstation. This will be used for analysis of RNAseq data (using Trinity and, later, Tuxedo), as well as...
Forum: Bioinformatics 09-25-2013, 01:47 PM
Replies: 3
Views: 2,126
Posted By anth
Thanks for your reply. The experiment has not...

Thanks for your reply. The experiment has not been undertaken yet - but there will absolutely be biological replicates for each condition. I have edited the original post to correct this.
Forum: Epigenetics 09-25-2013, 01:42 PM
Replies: 14
Views: 7,291
Posted By anth
Hello Olaf, Sorry to thread hijack. I'm very...

Hello Olaf,

Sorry to thread hijack. I'm very curious as to how you approach analysis. Following the methylation calls from Bismark, how do you identify differential methylation?

Thanks!
...
Forum: Bioinformatics 09-25-2013, 09:36 AM
Replies: 3
Views: 2,126
Posted By anth
Software tools for comparing entire methylomes (WGBS)

Software tools for comparing entire methylomes (WGBS)

I am currently exploring the possibility of comparing entire methylomes of genets exposed to two different conditions.

There seem to be a...
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