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Forum: Bioinformatics 10-10-2012, 02:15 AM
Replies: 8
Views: 2,961
Posted By pbrand
Strangely, I do not have entries in .ctg2read,...

Strangely, I do not have entries in .ctg2read, .readONcontig and .links..
It must have something to do with single-end paired-end libraries, because my config file doesn't seem to be incomplete.
...
Forum: Bioinformatics 10-10-2012, 12:34 AM
Replies: 8
Views: 2,961
Posted By pbrand
As I said, I haven't managed to get any splice...

As I said, I haven't managed to get any splice variants so I can't say anything about it ;)
I also haven't found a site with suitable information on the outputs, yet.
But there is a command that...
Forum: Bioinformatics 10-09-2012, 04:43 AM
Replies: 8
Views: 2,961
Posted By pbrand
Hi Jeremy, the variants, should be saved to the...

Hi Jeremy,
the variants, should be saved to the .scafSeq file. But with my data I didn't manage to get any of them. Maybe it is because I used single-end reads..
What kind of reads do you have?
...
Forum: Bioinformatics 07-25-2012, 09:16 AM
Replies: 8
Views: 2,961
Posted By pbrand
SOAPdenovo-trans alternative splicing

Hi,
I am working with several assemblers to find the best one for my RNA-Seq data.
Besides Trinity and Oases I used SOAPdenovo -trans.

While Oases found massive sequences that have possible...
Forum: Bioinformatics 06-21-2012, 01:15 AM
Replies: 5
Views: 4,421
Posted By pbrand
Hi Don, thanks for your post, it was really...

Hi Don,
thanks for your post, it was really helpful.

Regarding SOAP-trans what k-mer seems the best to you to use, as it has no multi-k function like oases? I am interested in the low and highly...
Forum: Bioinformatics 05-04-2012, 08:45 AM
Replies: 0
Views: 1,553
Posted By pbrand
Interesting Behavior: The megablast standalone behaves as blastn.. Who knows why???

Hi all,
I am using the blastn standalone with the MEGABLAST algorithm to find contaminations in my illumina Hymenopteran database prior to assembly.

I observed the interesting instance, that...
Forum: Bioinformatics 03-14-2012, 07:28 AM
Replies: 18
Views: 8,486
Posted By pbrand
Thanks a lot for your answers! Philipp

Thanks a lot for your answers!
Philipp
Forum: Bioinformatics 03-14-2012, 07:13 AM
Replies: 18
Views: 8,486
Posted By pbrand
Unfortunately, yes. But what we can do is trying...

Unfortunately, yes. But what we can do is trying to find out possible candidate DE - genes for realtime PCR. Therefore I wanted to follow the suggested way to estimate DE via estimated dispersion.
...
Forum: Bioinformatics 03-14-2012, 06:54 AM
Replies: 18
Views: 8,486
Posted By pbrand
because of our low budget, I have just two...

because of our low budget, I have just two samples with pooled RNA of 40 specimen each.
Forum: Bioinformatics 03-14-2012, 06:47 AM
Replies: 18
Views: 8,486
Posted By pbrand
So I can consider them as 'truly' differentially...

So I can consider them as 'truly' differentially expressed?

Can I say that I do not have DE, if all not-adjusted p-values which are significant show no significance anymore after adjustment?
Forum: Bioinformatics 03-14-2012, 06:07 AM
Replies: 18
Views: 8,486
Posted By pbrand
help: adjusted p-values in edgeR

Hi everybody,

I am relatively new to RNA-Seq and DE statistics. We have chosen to use edgeR for DE analysis and I understood most functions so far or I could answer them via searching the...
Forum: Bioinformatics 02-24-2012, 05:36 AM
Replies: 5
Views: 4,421
Posted By pbrand
Knowledge about SOAPdenovo-trans

Hi all,
I found a unpublished tool for transcriptome de novo assembly: SOAPdenovo-trans http://soap.genomics.org.cn/SOAPdenovo-Trans.html but I haven't found anything about it's performance in...
Forum: Introductions 02-24-2012, 05:24 AM
Replies: 0
Views: 686
Posted By pbrand
Hello

Hi,
I am a graduate student working with RNA-Seq of two sibling species and I am here to dig deeper in the matter of de novo assembly, DE and so on.

regards,
Philipp
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