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Search: Posts Made By: DerSeb
Forum: Bioinformatics 11-23-2015, 05:32 PM
Replies: 3
Views: 3,107
Posted By DerSeb
Dear Roman, feel free to contact me at: ...

Dear Roman,

feel free to contact me at:

sebastian.schaefer and at the domain nhcs.com.sg

Thanks for your interest in our work,
Sebastian
Forum: Bioinformatics 10-08-2015, 10:18 PM
Replies: 3
Views: 3,107
Posted By DerSeb
Hi yerbol, we have done just that: ...

Hi yerbol,

we have done just that:

http://onlinelibrary.wiley.com/doi/10.1002/0471142905.hg1116s87/abstract

There is also a script available that will calculate the PSI scores as explained...
Forum: Bioinformatics 10-08-2015, 10:13 PM
Replies: 1
Views: 1,145
Posted By DerSeb
Hi kajot, you can use this method that works...

Hi kajot,

you can use this method that works with any annotation:

http://onlinelibrary.wiley.com/doi/10.1002/0471142905.hg1116s87/abstract
Forum: Literature Watch 07-22-2015, 08:44 PM
Replies: 1
Views: 2,818
Posted By DerSeb
Quantifying gene expression at the level of translation: Ribo-seq in tissue

We performed ribosome profiling of the heart and liver of two inbred rat strains. Our results suggest that:

- Ribo-seq is a better proxy for protein levels than RNA-seq
- There is widespread...
Forum: Bioinformatics 05-08-2014, 06:09 AM
Replies: 11
Views: 2,603
Posted By DerSeb
For mapping I always use the Ensembl GTF...

For mapping I always use the Ensembl GTF annotation files, since they are less conservative and contain many possible transcripts.

I simply want to maximize the amount of splice junctions...
Forum: Bioinformatics 05-08-2014, 05:03 AM
Replies: 1
Views: 1,280
Posted By DerSeb
Extracting reads with a particular mismatch from bam file

Hi @ll,

I want to do the following and have not found any suggestions on the web yet:

I would like to extract reads from a bam file that contain a certain mismatch to the reference.

This...
Forum: Bioinformatics 03-18-2013, 06:19 AM
Replies: 0
Views: 1,193
Posted By DerSeb
Question Adjusting Allele Frequency when calling variants with bcftools

Hi all,

I'm currently using bcftools to call variants from NGS data. In my case the allele frequency of the variants is not always 50 or 100%, but can also be quite low (below 10%). However, the...
Forum: Bioinformatics 10-05-2012, 12:15 AM
Replies: 2
Views: 1,122
Posted By DerSeb
Hello Simon, thanks for your fast reply! ...

Hello Simon, thanks for your fast reply!

Yes, of course I have 45 samples... sorry for the confusion.

About the level of splicing: I am looking at zero, half and full expression of a splicing...
Forum: Bioinformatics 10-04-2012, 03:48 AM
Replies: 2
Views: 1,122
Posted By DerSeb
DEXseq, several factors influencing splicing

Dear all,

I would like to analyze RNAseq data with DEXseq and have questions regarding the model which is most appropriate for my approach.

Basicly, I have a timeline experiment with 5 time...
Forum: RNA Sequencing 05-15-2012, 12:31 AM
Replies: 3
Views: 3,562
Posted By DerSeb
Just a brief update: This errors were due to...

Just a brief update: This errors were due to bowtie2 beta5. Using beta6, everything works as expected.
Forum: RNA Sequencing 05-10-2012, 10:33 AM
Replies: 16
Views: 4,418
Posted By DerSeb
[QUOTE=Simon Anders;73143]No, this will produce...

[QUOTE=Simon Anders;73143]No, this will produce lots of false positives. If you present cuffdiff with a single control and a single treatment sample, it cannot estimate biological variation and will...
Forum: RNA Sequencing 05-10-2012, 09:26 AM
Replies: 16
Views: 4,418
Posted By DerSeb
yes, you are right in principle. the fragment...

yes, you are right in principle. the fragment counts are normalized.

however, no normalization works perfectly and this is a rather complex problem. therefor will give you different results for...
Forum: RNA Sequencing 05-10-2012, 06:56 AM
Replies: 16
Views: 4,418
Posted By DerSeb
If you need a fast and more conservative result,...

If you need a fast and more conservative result, I would suggest you compare one against one for both replicates and then take the overlap of both comparisons.

This way you reduce your false...
Forum: RNA Sequencing 05-10-2012, 12:41 AM
Replies: 5
Views: 2,414
Posted By DerSeb
hmm are the names of your contigs in the...

hmm are the names of your contigs in the annotation gff and the genome the same?

sometimes this happens when your reads map to say chromosome "1" and the gff has only chromosme "chr1"
Forum: RNA Sequencing 05-10-2012, 12:35 AM
Replies: 36
Views: 23,413
Posted By DerSeb
This would be my estimates, looking at human,...

This would be my estimates, looking at human, mouse or rat:

1. for a run of the mill (not looking for anything fancy, microarray replacement type of RNA-seq) 60M
2. a run looking for alternate...
Forum: RNA Sequencing 05-09-2012, 06:55 AM
Replies: 36
Views: 23,413
Posted By DerSeb
I think the deeper the better. No dataset has yet...

I think the deeper the better. No dataset has yet reached the maximum coverage needed to answer all questions.

If you want to only look at Gene expression, probably ~ 60 Million reads would be ok...
Forum: RNA Sequencing 05-09-2012, 04:47 AM
Replies: 3
Views: 3,562
Posted By DerSeb
Low mapping percentage with TopHat2

Hi all,

I'm currently looking at TopHat2 output and wonder if I will switch from Tophat 1 to Tophat 2. I like many of the new features of TopHat, but I still have some problems with the new...
Forum: Bioinformatics 02-15-2012, 02:22 AM
Replies: 2
Views: 1,124
Posted By DerSeb
Large scale cuffdiff analysis

Hi all,

already my second threat these days, but I have another question regarding analyzing RNA-seq data with the cufflinks package.

We have used cuffdiff and other approaches to look for...
Forum: Bioinformatics 02-14-2012, 04:47 AM
Replies: 46
Views: 16,641
Posted By DerSeb
New differential testing of cuffdiff/cufflinks since 1.3.0

Hi all,

I have been trying out the new 1.3 version of the cufflinks package to see if the testing for differential splicing/expression etc is improved.

Now I expected a more stringent analysis,...
Forum: Bioinformatics 06-17-2011, 02:10 AM
Replies: 6
Views: 10,534
Posted By DerSeb
Regarding your first question: The -D option...

Regarding your first question: The -D option keeps per sample read depth with mpileup.
Forum: Bioinformatics 01-17-2011, 06:05 AM
Replies: 0
Views: 1,112
Posted By DerSeb
Counting reads that jump over a position

Dear all,

I would like to count reads that are present before a feature and after a feature, but not in the feature. My Input is a *.bam file and the features are exon described in .gtf format.
...
Forum: Bioinformatics 01-17-2011, 06:01 AM
Replies: 4
Views: 10,224
Posted By DerSeb
What I like to di is to count the flags that are...

What I like to di is to count the flags that are present:

samtools view *.bam | awk ' { per[$2] += 1 }END { for (i in per)print i, per[i] }

This command will show you which flags are present...
Forum: Bioinformatics 01-13-2011, 11:31 AM
Replies: 2
Views: 1,985
Posted By DerSeb
Using split/merge .bams for Cufflinks

Dear all,

today I have a question regarding splitting and merging of .bam files as input for cufflinks.

For speeding up my calculations and trying different parameters, I have split and merged...
Forum: Bioinformatics 12-21-2010, 06:06 AM
Replies: 4
Views: 2,738
Posted By DerSeb
great, I tried it and it works! thx!

great, I tried it and it works!

thx!
Forum: Bioinformatics 12-13-2010, 01:30 PM
Replies: 4
Views: 2,738
Posted By DerSeb
Tophat SOLID PE data not mapped in pairs

Hello,

this is a problem I have been dealing with now for a long time. I try to map SOLID PE reads using TopHat v 1.1.4 using this command:

tophat --color --quals -r 155 -p 4 -o /data/genetics/...
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