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Forum: Illumina/Solexa 12-15-2014, 06:14 AM
Replies: 18
Views: 13,207
Posted By moritzhess
Hi Simon, thank's for your response. That's...

Hi Simon,

thank's for your response. That's very interesting I might need to study the matter more in detail to fully understand.
Moritz
Forum: Illumina/Solexa 12-15-2014, 04:48 AM
Replies: 18
Views: 13,207
Posted By moritzhess
I now this answer is really late ;). I thought...

I now this answer is really late ;). I thought that even if it is possible to introduce a "batch factor" as fixed effect, one would loose a lot of power because more degrees of freedom are consumed...
Forum: Illumina/Solexa 04-09-2014, 12:57 PM
Replies: 18
Views: 13,207
Posted By moritzhess
I would not necessary consider this design...

I would not necessary consider this design super-simple. At least the fact that you have multiple measurements per individual might be a little tricky because of a high amount of dependency...
Forum: Bioinformatics 07-23-2013, 05:50 AM
Replies: 8
Views: 9,002
Posted By moritzhess
As far as I know, you have to tell DESEQ to treat...

As far as I know, you have to tell DESEQ to treat all expression values as if they were emerging from a single condition by specifying method="blind" when extimating the Dispersions.
Forum: Illumina/Solexa 03-20-2013, 06:52 AM
Replies: 18
Views: 13,207
Posted By moritzhess
ShrinkSeq ...

ShrinkSeq http://www.few.vu.nl/~mavdwiel/ShrinkBayes.html , seems to be very flexible and allows for random effects.
Forum: Bioinformatics 01-13-2013, 03:53 AM
Replies: 3
Views: 1,444
Posted By moritzhess
Problem solved by upgrading to Version 2.0.5.

Problem solved by upgrading to Version 2.0.5.
Forum: Bioinformatics 12-27-2012, 02:58 AM
Replies: 3
Views: 1,444
Posted By moritzhess
Hi Luyi Tian, thanks for your fast response! ...

Hi Luyi Tian,
thanks for your fast response!
The program itself is quiet but I piped the bowtie output to samtools view to generate bam files and samtools reports: "Parse error at line 1299638:...
Forum: Bioinformatics 12-27-2012, 01:24 AM
Replies: 3
Views: 1,444
Posted By moritzhess
bowtie2 stops during alignment

Hi everybody,

I am aligning Illumina 100bp reads to a reference transcriptome using bowtie2. When aligning certain fastq files, bowtie stops aligning always at the same position. The first read,...
Forum: Bioinformatics 10-11-2012, 07:56 AM
Replies: 2
Views: 1,430
Posted By moritzhess
Hi Sammy07, could you already find out if...

Hi Sammy07,

could you already find out if ssaha2 (or anybody else) can output unmapped reads in sam format ?
I would also be very interested in such an option.

Moritz
Forum: Bioinformatics 10-11-2012, 04:46 AM
Replies: 1
Views: 766
Posted By moritzhess
I do not know if this of great help, but if you...

I do not know if this of great help, but if you are a little bit familiar with python (really just a little bit), the HTSEQ (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) package...
Forum: Bioinformatics 12-23-2011, 01:51 AM
Replies: 16
Views: 10,948
Posted By moritzhess
In my opinion the most convenient and sensitive...

In my opinion the most convenient and sensitive but also potentially slowest way is to align the illumina adapters using e.g. SSAHA2 which will even detect adapters when there is a rather high error...
Forum: Bioinformatics 09-05-2011, 11:31 AM
Replies: 2
Views: 2,335
Posted By moritzhess
@nilshomer: Thank's! I have to try that...

@nilshomer:

Thank's! I have to try that option! (just how to see how fast slooow is). But now the diagrams make more sense.
Forum: Bioinformatics 09-05-2011, 04:57 AM
Replies: 21
Views: 7,082
Posted By moritzhess
Maybe you try bfast or ssaha. They are not very...

Maybe you try bfast or ssaha. They are not very fast but should perform ways better on your data. Bfast seems to be faster (from what I heard) but I think ssaha is a good startingpoint to get a first...
Forum: Bioinformatics 09-05-2011, 02:19 AM
Replies: 2
Views: 2,335
Posted By moritzhess
BWA:high amount of unique alignments despite high mismatch tolerance

Hi, I am a little puzzled by my data. I aligned 100bp Illumina 3' tags to a reference transcriptome generated from 454 Data using BWA. The Reference has been created using NEwbler, so the reference...
Forum: Sample Prep / Library Generation 04-19-2011, 08:11 AM
Replies: 7
Views: 4,231
Posted By moritzhess
Hi Amango, Thank you very much! Actually...

Hi Amango,

Thank you very much! Actually I've always wondered if this kind of modification of the protocol works out and it seems to work out pretty well.
Moritz
Forum: RNA Sequencing 04-05-2011, 02:57 PM
Replies: 4
Views: 1,939
Posted By moritzhess
It's good to hear that the method cited is not...

It's good to hear that the method cited is not too complicated because I m really tempted to use their technique. We have a reference transcriptome. If I got you right, many transcripts in our...
Forum: RNA Sequencing 04-05-2011, 09:36 AM
Replies: 4
Views: 1,939
Posted By moritzhess
Hi Genlyai, thanks for your response ! I...

Hi Genlyai,

thanks for your response ! I heard that Illumina disconitued the DGE Kits. Furthermore as far as I know, the tags are only 20bp long, which could be a problem, because we don't have a...
Forum: RNA Sequencing 04-05-2011, 03:48 AM
Replies: 4
Views: 1,939
Posted By moritzhess
Custom SAGE with RNA SEQ Kit

Hi,
I posted this in the library prep forum but I assume it might fit in here better:

I want to use the Illumina TruSEq Kit for SAGE analysis: getting only one read per transcript. To achieve...
Forum: Sample Prep / Library Generation 04-05-2011, 03:14 AM
Replies: 7
Views: 4,231
Posted By moritzhess
I Uploaded a picture to outline the method (it's...

I Uploaded a picture to outline the method (it's horrible I know!) I wan't to apply. Basically the only modifications are to switch fragmentation and enrichment steps and to use polyT primers for...
Forum: Sample Prep / Library Generation 03-24-2011, 12:34 AM
Replies: 7
Views: 4,231
Posted By moritzhess
I do not have access to that paper, so I could...

I do not have access to that paper, so I could not checkout. But in the meantime I just remembered that I heard somewhere that to only sequence the most 3' prime part of a transcript it would be...
Forum: Sample Prep / Library Generation 03-23-2011, 06:32 AM
Replies: 7
Views: 4,231
Posted By moritzhess
Hi Steven, thank you very much ! This...

Hi Steven,

thank you very much ! This Helicos stuff is really interesting, especially in terms of sample prep. Nevertheless we are a little bit "tied" to Illumina Seq as "our" Seq facility "only"...
Forum: Sample Prep / Library Generation 03-22-2011, 09:00 AM
Replies: 7
Views: 4,231
Posted By moritzhess
3' RNA Seq libraries (creating tags)

Hi,
we are planning to profile gene expression in a number of samples. We are not investigating an organism without genome sequence (but reference transcriptome) available. In order to save costs we...
Forum: Introductions 02-07-2011, 05:29 AM
Replies: 8
Views: 5,498
Posted By moritzhess
SOAP denovo has also been used for transcriptome...

SOAP denovo has also been used for transcriptome assembly:

"De Novo Analysis of Transcriptome Dynamics in the Migratory Locust during the Development of Phase Traits"

I would also recommend a...
Forum: Sample Prep / Library Generation 11-06-2010, 01:38 PM
Replies: 0
Views: 2,458
Posted By moritzhess
Experience with nugen ovation 3 dge System

Hi everyone,

I am very interested in tag based RNA Seq and are therefore curious if anyone of you already have used this kit and how your experiences are with the system ?

Thanks in advance
...
Forum: Sample Prep / Library Generation 08-29-2010, 03:24 PM
Replies: 0
Views: 1,529
Posted By moritzhess
Generation of 3' directed cDNA libraries

Hi,
we're planning to investigate the transcriptome of a conifer species. It is intended to construct 3' directed cDNA libraries, preferentially by random fragmentation that will be sequenced on...
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