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Search: Posts Made By: ffinkernagel
Forum: Bioinformatics 10-23-2014, 12:59 PM
Replies: 1
Views: 728
Posted By ffinkernagel
I don't know rpy2-bioconductor - and don't see...

I don't know rpy2-bioconductor - and don't see the benefit either.

I've been using R and bioconductor via rpy2 for years now - it's a solid combo, especially in combination with pandas.
Forum: RNA Sequencing 07-15-2014, 01:53 AM
Replies: 12
Views: 3,905
Posted By ffinkernagel
A t-test is dependend on the effect size - and...

A t-test is dependend on the effect size - and that obviously changes if you do log2.
The general rule is to test on the data you measure - in this case, this would be the un-logged reads per...
Forum: Bioinformatics 03-12-2014, 12:32 AM
Replies: 6
Views: 2,993
Posted By ffinkernagel
You know because a library of a million...

You know because a library of a million 'effective reads' (after dedup) distributed in the largish genome of a mammal isn't useful, and no antibody is so good that you'll only get the enriched...
Forum: Illumina/Solexa 02-10-2014, 10:53 AM
Replies: 4
Views: 1,673
Posted By ffinkernagel
You can try an assembly and blasting the results....

You can try an assembly and blasting the results.

Possible it's fish dna from the bead blocking.
Forum: Bioinformatics 01-27-2014, 05:36 AM
Replies: 5
Views: 1,243
Posted By ffinkernagel
ECC guards against bit errors in RAM - these are...

ECC guards against bit errors in RAM - these are rare in the first place, and if they occur will most likely just flip one of the bases in your reads - depending on the encoding possibly even to...
Forum: Bioinformatics 01-09-2014, 06:57 AM
Replies: 10
Views: 7,132
Posted By ffinkernagel
Not disk space, RAM - STAR uses quite a lot of...

Not disk space, RAM - STAR uses quite a lot of ram to generate it's index (last time I checked, 16 GB were not enough for a human genome)
Forum: Bioinformatics 01-07-2014, 11:41 PM
Replies: 10
Views: 7,132
Posted By ffinkernagel
How much memory do you have?

How much memory do you have?
Forum: Bioinformatics 01-06-2014, 11:32 PM
Replies: 10
Views: 7,132
Posted By ffinkernagel
The genomes you can download from the STAR...

The genomes you can download from the STAR website have already been prepared - no need to run genomeGenerate on them again. Just skip ahead to the alignment stage.
Forum: General 11-20-2013, 06:04 AM
Replies: 9
Views: 5,712
Posted By ffinkernagel
Do not underestimate your customer base.

Do not underestimate your customer base.
Forum: General 11-19-2013, 07:35 AM
Replies: 9
Views: 5,712
Posted By ffinkernagel
Your software won't run anymore, because you...

Your software won't run anymore, because you pulled the plug.

Biologists will routinely revisit data that was generated a few years ago and now want to either fiddle with parameters or analyze...
Forum: General 11-19-2013, 06:41 AM
Replies: 9
Views: 5,712
Posted By ffinkernagel
You just excluded anybody being serious about...

You just excluded anybody being serious about reproducability from using your software.
Not only is it a black box, no now it's a black box guranteed to stop working at some uncertain point in time....
Forum: Bioinformatics 11-12-2013, 11:19 PM
Replies: 2
Views: 1,352
Posted By ffinkernagel
It's not straight forward, since you'll need to...

It's not straight forward, since you'll need to retrieve all the exons and join them by hand.
Here's a bit of Python + SQL that yields all transcript_id->cDNA pairs - I'm sure you can adapt it...
Forum: Bioinformatics 10-11-2013, 06:46 AM
Replies: 2
Views: 1,773
Posted By ffinkernagel
You can do a Monte carlo against randomly...

You can do a Monte carlo against randomly distributed regions, or even regions randomly distributed that are still the same distance to TSS or such. Will basically always call your result significant...
Forum: Bioinformatics 08-12-2013, 07:46 AM
Replies: 10
Views: 4,191
Posted By ffinkernagel
Barplots are nice, but they do hide the original...

Barplots are nice, but they do hide the original intensities measured.

What were your genes ct and absolute tag counts (out of how many reads)?
Forum: Epigenetics 08-09-2013, 01:05 AM
Replies: 5
Views: 5,072
Posted By ffinkernagel
Start with the peaks with the most reads. Well,...

Start with the peaks with the most reads. Well, actually, skip the first 10 or so that have x-thousand reads - they're usually artifacts. You're looking for something in the 95%th but not in the...
Forum: Epigenetics 08-09-2013, 12:38 AM
Replies: 5
Views: 5,072
Posted By ffinkernagel
MACS FDR is heavily influcenced by what your...

MACS FDR is heavily influcenced by what your background looks like, and I've seen many a decent chipseq lane where the FDR was utterly unusable.

Plus it has the amazing property that stronger...
Forum: Bioinformatics 08-14-2012, 05:46 AM
Replies: 20
Views: 22,197
Posted By ffinkernagel
You are mistaken. The reads only contain a number...

You are mistaken. The reads only contain a number that tells which entry from the header to pick.
Forum: General 07-27-2012, 02:53 AM
Replies: 5
Views: 3,016
Posted By ffinkernagel
log(a / b) = log(a) - log(b), so you can do...

log(a / b) = log(a) - log(b),

so you can do what you're proposing, but you have to substract the two logs, not divide them.
Forum: Bioinformatics 07-26-2012, 03:34 AM
Replies: 3
Views: 1,880
Posted By ffinkernagel
Indeed - but then at least for myc I know that...

Indeed - but then at least for myc I know that the antibody is pretty decent.
Forum: Bioinformatics 07-26-2012, 03:00 AM
Replies: 3
Views: 1,880
Posted By ffinkernagel
A) Very much so. B) Either that or your ChIP...

A) Very much so.
B) Either that or your ChIP did not work.
C) Very much depends on the antibody, and the portion of the genome covered by your factor. For those two, I'd start at minimum of 20...
Forum: Bioinformatics 06-28-2012, 12:09 AM
Replies: 1
Views: 1,355
Posted By ffinkernagel
Do you have write permissions it this directory?

Do you have write permissions it this directory?
Forum: Bioinformatics 06-24-2012, 02:53 AM
Replies: 3
Views: 1,409
Posted By ffinkernagel
Bowtie considers a 'N' in a read a mismatch - to...

Bowtie considers a 'N' in a read a mismatch - to quote the manual 'Ambiguous characters in the read mismatch all other characters.'

Depending on how you sampled the reads, that might explain 0 to...
Forum: Bioinformatics 04-11-2012, 08:02 AM
Replies: 5
Views: 1,808
Posted By ffinkernagel
Hm. Sounds to me like a very low complexity...

Hm. Sounds to me like a very low complexity library - I have seen one or two of those, but can only speculate about the reason.
Perhaps very low amounts of input dna with too many PCR cycles?
Forum: Bioinformatics 03-29-2012, 05:57 AM
Replies: 3
Views: 5,173
Posted By ffinkernagel
My guess: you have reads that were mapped to...

My guess: you have reads that were mapped to multiple locations, and htseq doesn't remove duplicates.

You should get the same count if you drop the uniq form your command line (which amounts just...
Forum: Bioinformatics 03-13-2012, 05:17 AM
Replies: 3
Views: 2,107
Posted By ffinkernagel
@turnersed: Guess the first question is whether...

@turnersed: Guess the first question is whether they're real 'novel' isoforms, or had already been in Ensembl.
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