Moderator: Stefano Berri
Stefano Berri ♦ 4.0k
- Reputation:
- 4,020
- Status:
- Trusted
- Location:
- Cambridge, UK
- Website:
- http://www.stefanoberr...
- Twitter:
- @5tefano8erri
- Scholar ID:
- Google Scholar Page
- Last seen:
- 11 months, 2 weeks ago
- Joined:
- 8 years, 2 months ago
- Email:
- s*****@illumina.com
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
<prev
• 123 results •
page 1 of 13 •
next >
0
votes
1
answer
875
views
1
answers
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 14 months ago by
Stefano Berri ♦ 4.0k
0
votes
1
answer
725
views
1
answers
... I am getting this message: "CWL Directory inputs not yet supported in Toil" ...
written 15 months ago by
Stefano Berri ♦ 4.0k
3
votes
1
answer
725
views
1
answer
... 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 15 months ago by
Stefano Berri ♦ 4.0k
• updated
12 months ago by
Biostar ♦♦ 20
0
votes
0
answers
1.6k
views
0
answers
Comment:
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 4.2 years ago by
Stefano Berri ♦ 4.0k
5
votes
11
answers
2.5k
views
11
answers
... 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.
...
written 4.2 years ago by
Stefano Berri ♦ 4.0k
0
votes
1
answer
1.7k
views
1
answers
... 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 4.4 years ago by
Stefano Berri ♦ 4.0k
0
votes
1
answer
1.7k
views
1
answers
... 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 4.4 years ago by
Stefano Berri ♦ 4.0k
1
vote
1
answer
1.7k
views
1
answers
... 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 4.4 years ago by
Stefano Berri ♦ 4.0k
1
vote
4
answers
3.8k
views
4
answers
... 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 4.5 years ago by
Stefano Berri ♦ 4.0k
0
votes
4
answers
3.8k
views
4
answers
... yes, that might work actually... column 2 and 3 are always number in the content, but never in browser or track...
...
written 4.5 years ago by
Stefano Berri ♦ 4.0k
Latest awards to Stefano Berri
Librarian
12 months ago,
created a post with more than 10 bookmarks.
For Read Group In Sam/Bam Files: What Do They Exactly Describe?
Popular Question
3.4 years ago,
created a question with more than 1,000 views.
For Read Group In Sam/Bam Files: What Do They Exactly Describe?
Teacher
3.4 years ago,
created an answer with at least 3 up-votes.
For A: Gatk Pipeline: Markduplicates At The End ?
Great Question
3.4 years ago,
created a question with more than 5,000 views.
For Read Group In Sam/Bam Files: What Do They Exactly Describe?
Appreciated
3.4 years ago,
created a post with more than 5 votes.
For A: Normal Distribution Of (Log) Microarray Results
Good Answer
3.4 years ago,
created an answer that was upvoted at least 5 times.
For A: Creating A New Bioinformatics Unit
Teacher
3.4 years ago,
created an answer with at least 3 up-votes.
For A: How To Handle Replicates With Huge Differences In Number Of Reads?
Student
3.4 years ago,
asked a question with at least 3 up-votes.
For Read Group In Sam/Bam Files: What Do They Exactly Describe?
Epic Question
3.4 years ago,
created a question with more than 10,000 views.
For Read Group In Sam/Bam Files: What Do They Exactly Describe?
Great Question
3.4 years ago,
created a question with more than 5,000 views.
For How To Produce Simulated 'Synthetic' Sequences
Appreciated
3.4 years ago,
created a post with more than 5 votes.
For A: Creating A New Bioinformatics Unit
Appreciated
3.4 years ago,
created a post with more than 5 votes.
For A: Genomic Read Mapping Biased Towards Coding Regions?
Appreciated
3.4 years ago,
created a post with more than 5 votes.
For A: Find A Substring And Count The Number Of Occurrences
Prophet
3.4 years ago,
created a post with more than 20 followers.
For Read Group In Sam/Bam Files: What Do They Exactly Describe?
Great Question
3.7 years ago,
created a question with more than 5,000 views.
For Read Group In Sam/Bam Files: What Do They Exactly Describe?
Good Answer
4.0 years ago,
created an answer that was upvoted at least 5 times.
For A: Communicating With Non-Computational Biologists
Commentator
4.0 years ago,
created a comment with at least 3 up-votes.
For C: What'S "Allelic Ratio"? Can It Equal 1 In Normal Cells?
Appreciated
4.2 years ago,
created a post with more than 5 votes.
For A: What'S "Allelic Ratio"? Can It Equal 1 In Normal Cells?
Teacher
4.2 years ago,
created an answer with at least 3 up-votes.
For A: Best Practices For Pipeline Versioning
Teacher
4.3 years ago,
created an answer with at least 3 up-votes.
For A: Determine Whether A Gene Product Is A Transcription Factor
Guru
4.3 years ago,
received more than 100 upvotes.
Teacher
4.3 years ago,
created an answer with at least 3 up-votes.
For A: Technical/Biological Replicates In Rna-Seq For Two Cell Lines
Centurion
4.3 years ago,
created 100 posts.
Voter
4.3 years ago,
voted more than 100 times.
Teacher
4.3 years ago,
created an answer with at least 3 up-votes.
For A: List Of Freely Available Tool/Software To Generate Rooted Phylogeneitc Tree
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 639 users visited in the last hour