Moderator: Stefano Berri
Stefano Berri ♦ 3.9k
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- Cambridge, UK
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- http://www.stefanoberr...
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- @5tefano8erri
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Trained in molecular biology I slowly moved to the computational side and data anlysis of genomic data. I am now a bioinformatics scientist working at Illumina within the "Population and Medical Genomics" group. My interests are in genomics, molecular biology, cancer biology, tumour evolution and reproducible science. I regularly use R/Bioconductor, Python, SQL I know a thing or two about copy number abnormalities in cancer and I develop tools to analyse Next Generation Sequencing data.
Posts by Stefano Berri
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Comment:
C: CWL: Loops and if conditionals
... I am a beginner with cwl, but here my approach to conditional events. Make the workflow linear, like this:
Inspect data
|
Preprocess-Required?
|
Pre-process data
|
Process Data
L'et's say that Preprocess-Required spit out a file with "YES" or "NO"
Then preprocess data read that file ...
written 4 months ago by
Stefano Berri ♦ 3.9k
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... I am getting this message: "CWL Directory inputs not yet supported in Toil" ...
written 4 months ago by
Stefano Berri ♦ 3.9k
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... I am experimenting with CWL and cwltool. I have successfully written a workflow that can scatter jobs. However, cwltool runs them sequencially, whereas I would like to to use the Sun Grid Engine (SGE) to run jobs in parallel. I looked into Toil to run it but I have found it not capable of running th ...
written 4 months ago by
Stefano Berri ♦ 3.9k
• updated
11 weeks ago by
Biostar ♦♦ 20
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C: CNV from FFPE genomes
... Can I ask you what tools you used, what is the typical coverage, if you use a match normal (and if so, if you use same library prep) and if the tools you used perform GC correction. These are the first relevant questions that pop in my mind...
...
written 3.4 years ago by
Stefano Berri ♦ 3.9k
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... Hi.
I think there are quite few "pure biologist" that turned to the darks side of bioinformatics, and I am one of them. I didn't have any formal training in programming/informatics till the end of my Ph.D. in molecural biology. For sure, all you knowledge in biology is not wasted. It is an asset.
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written 3.4 years ago by
Stefano Berri ♦ 3.9k
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... 50M reads is quite a lot, actually. In CNAnorm all windows are equally sized. If you set 10Kbp windows, you would get an average of 170 reads per window. Which is plenty.
From a quick count, 85% of exons are less than 10Kbp apart, and 93% less than 25kbp apart, so most of your windows will have som ...
written 3.5 years ago by
Stefano Berri ♦ 3.9k
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... Hi. exome is a bit more tricky becose is uneven, but as a rule of thumb, try to have, as average, 50 reads per window. In gene rich regions you will have more, in gene poor a bit less. HOw many reads do you have in total? Good luck.
Stefano
...
written 3.5 years ago by
Stefano Berri ♦ 3.9k
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... Hi. You don't need high coverage data for copy number detection at the resolution of arrays.
You could use CNAnorm. It is designed to detect somatic CNA from low coverage genomic data (2 Million reads would be enough, very affordable if you multiplex on a run) and it does not assumes a particular r ...
written 3.5 years ago by
Stefano Berri ♦ 3.9k
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... thanks, if that is the case, then it's not too hard. I haven't found a documents that "officially" states something like that, though...
...
written 3.7 years ago by
Stefano Berri ♦ 3.9k
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... yes, that might work actually... column 2 and 3 are always number in the content, but never in browser or track...
...
written 3.7 years ago by
Stefano Berri ♦ 3.9k
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