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Forum: Academic/Non-Profit Jobs 05-22-2013, 04:23 AM
Replies: 0
Views: 1,125
Posted By mudshark
Postdoctoral Position in a Bioinformatics Competence Center, LM University, Munich

We wish to recruit a Bioinformatician/Biologist on a vacant position from 1st of Juli 2013 for 4 years to support research in a highly stimulating research network.


Job profile

As part of a...
Forum: Bioinformatics 03-19-2013, 09:57 AM
Replies: 1
Views: 1,109
Posted By mudshark
i would not work with peaks but rather with read...

i would not work with peaks but rather with read summarization on gene bodies (which are the span of H3K36me3 enrichment). Then you can use DESeq or EdgeR/limma to do your testing for differential...
Forum: Bioinformatics 02-26-2013, 08:59 AM
Replies: 13
Views: 2,905
Posted By mudshark
"ALL genes" is probably not a good background...

"ALL genes" is probably not a good background set. "ALL expressed genes" should be the universe.
Forum: Bioinformatics 02-21-2013, 11:49 PM
Replies: 13
Views: 2,905
Posted By mudshark
i usually fetch the latest annotations here:...

i usually fetch the latest annotations here: http://www.geneontology.org/GO.downloads.annotations.shtml
Forum: Bioinformatics 02-20-2013, 02:09 AM
Replies: 10
Views: 4,840
Posted By mudshark
can you provide a scatterplot a$V4 vs b$V4...

can you provide a scatterplot a$V4 vs b$V4 (probably best to subsample)?

just 2 additional cents: pearson correlations do not provide much information on the similarity of ChIPSeq samples given...
Forum: General 01-27-2013, 11:09 PM
Replies: 5
Views: 1,745
Posted By mudshark
sounds good. everything controlled. in case you...

sounds good. everything controlled. in case you want to save some bucks i would skip the da-GAL4>UAS-TF_Flag precipated with IGM mouse
Forum: General 01-22-2013, 01:08 AM
Replies: 5
Views: 1,745
Posted By mudshark
the input is not equal to genomic DNA sequencing...

the input is not equal to genomic DNA sequencing as the release of DNA fragments in chromatin preps varies locally. depending on the activity status of chromatin, i.e. transcribed regions are...
Forum: General 01-20-2013, 11:56 PM
Replies: 5
Views: 1,745
Posted By mudshark
I'd say 1) Input control 2) FLAG in wt. Not...

I'd say
1) Input control
2) FLAG in wt. Not preferred as it is a different chromatin prep and in the worst case the FLAG-TF and wt flies might have local copy number variations.
Forum: Epigenetics 12-11-2012, 11:30 AM
Replies: 1
Views: 3,389
Posted By mudshark
about 9000-10000 USD

about 9000-10000 USD
Forum: Bioinformatics 12-04-2012, 04:35 AM
Replies: 3
Views: 1,697
Posted By mudshark
interesting question.. looking forward to some...

interesting question.. looking forward to some answers.

that's because I think there is no such normalization..
Forum: Bioinformatics 11-28-2012, 01:41 AM
Replies: 2
Views: 2,977
Posted By mudshark
in principle you just need strand-specific...

in principle you just need strand-specific coverage vectors of your ChIP signals and use the 'ccf' function in R to cross-correlate the two.


some remarks:
- why do you expect 570 bp?
- I once...
Forum: Sample Prep / Library Generation 10-17-2012, 06:05 AM
Replies: 4
Views: 50,483
Posted By mudshark
you should try to fully exploit the power of...

you should try to fully exploit the power of biological replication by full independence of experiments. do the replicates on different days with different batches of embryos and - ideally -...
Forum: Sample Prep / Library Generation 10-17-2012, 03:52 AM
Replies: 4
Views: 50,483
Posted By mudshark
some immediate thoughts: a) try to keep the...

some immediate thoughts:

a) try to keep the experiment as simple as possible. why 5 timepoints? (1) costs (2) statistical analysis incorporating all the data is fairly complicated. why not do a...
Forum: Bioinformatics 10-06-2012, 02:19 AM
Replies: 6
Views: 4,507
Posted By mudshark
i think CisGenome...

i think CisGenome (www.biostat.jhsph.edu/~hji/cisgenome/) can do exactly what you want.
Forum: Bioinformatics 08-30-2012, 01:03 AM
Replies: 1
Views: 1,258
Posted By mudshark
if your modifications do not localize to a...

if your modifications do not localize to a specific part of the genes
get average ChIPSeq counts for each gene and correlate with expression values

if your modifications do localize to a...
Forum: Bioinformatics 08-16-2012, 07:31 AM
Replies: 4
Views: 3,379
Posted By mudshark
its a transcription factor (unpublished). i...

its a transcription factor (unpublished).

i was thinking.. did you filter multiple hit reads? if not, these would explain the high coverages in input and MeDiP sample kind of obscuring the 'true'...
Forum: Bioinformatics 08-16-2012, 04:05 AM
Replies: 4
Views: 3,379
Posted By mudshark
a good chipseq expt looks like this using your...

a good chipseq expt looks like this using your code
http://i.imgur.com/cYmMa.png
Forum: Sample Prep / Library Generation 08-01-2012, 11:38 PM
Replies: 10
Views: 3,575
Posted By mudshark
We stopped using the Bioruptor(s) due to...

We stopped using the Bioruptor(s) due to performance decreases and irreproducible sonication results and bought a Covaris.
Forum: Bioinformatics 07-29-2012, 03:42 AM
Replies: 12
Views: 2,852
Posted By mudshark
if there is a clear peak summit try to use this...

if there is a clear peak summit try to use this position for getting a one-to-one relationship
Forum: Bioinformatics 07-27-2012, 07:27 AM
Replies: 12
Views: 2,852
Posted By mudshark
if it covers introns and exons it basically...

if it covers introns and exons it basically covers genes, your feature definition might be too fine grained.
Forum: Bioinformatics 07-25-2012, 07:04 AM
Replies: 1
Views: 917
Posted By mudshark
http://www.ncbi.nlm.nih.gov/sra/

http://www.ncbi.nlm.nih.gov/sra/
Forum: Epigenetics 07-24-2012, 11:27 PM
Replies: 3
Views: 1,864
Posted By mudshark
those operations are pretty straight forward...

those operations are pretty straight forward using IRanges in bioconductor. Have a look at the findOverlaps function for example.

I would be very careful with any normalization as there is no...
Forum: Bioinformatics 07-24-2012, 12:00 AM
Replies: 3
Views: 1,294
Posted By mudshark
to the best of my knowledge there is no...

to the best of my knowledge there is no established and validated tool to perform this task.

however, one straight-forward approach would be to collect the sum the reads on all genes in IP and...
Forum: MGISEQ (FKA Complete Genomics) 05-21-2012, 11:17 PM
Replies: 3
Views: 2,992
Posted By mudshark
if you can provide an appropriate file format,...

if you can provide an appropriate file format, e.g. wig, you can visualize the entire genome (at least in IGB)
Forum: Bioinformatics 05-08-2012, 07:41 AM
Replies: 1
Views: 1,819
Posted By mudshark
wonder if this is the correct forum to ask...

wonder if this is the correct forum to ask microarray questions

anyway i suggest to start with a bioconductor functions such as colSummarizeMedianpolish in the preprocessCore package that is more...
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