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Search: Posts Made By: shanebrubaker
Forum: Bioinformatics 08-01-2013, 11:36 AM
Replies: 1
Views: 791
Posted By shanebrubaker
I am wondering about this too. Has anyone ever...

I am wondering about this too. Has anyone ever tried looking at domains in a fused gene that do not seem to belong together perhaps?
Forum: Bioinformatics 07-19-2013, 01:31 PM
Replies: 0
Views: 912
Posted By shanebrubaker
Augustus training questions

Hi, I have a few questions about training Augustus:

1) is etraining something new that supercedes autoAug?
2) Are the training genes expected to be essentially highly curated, manually annotated...
Forum: Bioinformatics 07-01-2013, 12:59 PM
Replies: 1
Views: 601
Posted By shanebrubaker
Splitting Fused genes

Hi, I am using software such as cufflinks to create transcriptome assemblies. However, I have a very compact genome, and so end up with a lot of long, fused transcripts, often containing 2 or more...
Forum: Bioinformatics 11-20-2012, 05:02 PM
Replies: 2
Views: 940
Posted By shanebrubaker
That looks interesting, I will try it. Thanks!

That looks interesting, I will try it. Thanks!
Forum: Bioinformatics 10-30-2012, 10:25 AM
Replies: 2
Views: 807
Posted By shanebrubaker
Representative Transcripts

Hi, I want to take transcriptomes from different time points and pick the best or longest representative examples for given genes to create a collapsed set of transcripts (to use as a reference) and...
Forum: Pacific Biosciences 09-17-2012, 10:01 AM
Replies: 31
Views: 12,849
Posted By shanebrubaker
Hi, I am trying to run pacbiotoca. I am running...

Hi, I am trying to run pacbiotoca. I am running a small test, with 10 pacbio sequences to correct, against a set of Illumina data that is 37GB. It has now been running for nearly 4 days, on a...
Forum: Pacific Biosciences 09-14-2012, 03:08 PM
Replies: 55
Views: 19,484
Posted By shanebrubaker
I also noticed that you say it corrects the reads...

I also noticed that you say it corrects the reads to a 5% error rate, but the Schatz work seems to mention a 0.1% error rate. Is there a reason for that?

Thanks,
Shane
Forum: Bioinformatics 09-14-2012, 03:07 PM
Replies: 2
Views: 940
Posted By shanebrubaker
Pick a representative transcript

Hi, I would like a program to pick a representative subset of transcripts from different a set of multiple time point transcriptome assemblies. So in other words, I don't want the same transcript...
Forum: Pacific Biosciences 09-14-2012, 02:28 PM
Replies: 55
Views: 19,484
Posted By shanebrubaker
More Info on LSC

Hi, I am also very interested in LSC. I would like to see the paper and manual if they are available.

Does anyone have time comparisons of LSC vs. PacBioToCA vs. SmrtPipe?
Forum: Pacific Biosciences 09-14-2012, 10:32 AM
Replies: 31
Views: 12,849
Posted By shanebrubaker
I also have some questions about pacbiotoca. ...

I also have some questions about pacbiotoca. Mine is taking a long time as well. I have tried the spec file above.
Is there any way to estimate how long it should take?
Can anyone help maybe give...
Forum: Bioinformatics 08-03-2012, 03:10 PM
Replies: 2
Views: 2,897
Posted By shanebrubaker
Obtain file from Bowtie containing only aligned reads in SAM format

Hi, I have been using bowtie with the -S option to align reads to a reference sequence, and get SAM file as the output.

What I want is to get ONLY the aligned reads in the output. Instead I get...
Forum: Bioinformatics 05-11-2012, 01:54 PM
Replies: 9
Views: 4,727
Posted By shanebrubaker
On a related note, I was trying to reduce my data...

On a related note, I was trying to reduce my data size by using khmer, from a paper on Digitial Normalization. Does anyone have experience with this tool? I am getting an error when using it where...
Forum: Bioinformatics 01-19-2011, 01:43 PM
Replies: 3
Views: 2,447
Posted By shanebrubaker
Response to reverse complement question

I'm not sure if anyone ever answered this. Yes reads from Illumina Mate Pair (long-insert) libraries should be reverse-complemented for velvet. Other assemblers might be different.
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