Moderator: Jarretinha

gravatar for Jarretinha
Jarretinha3.2k
Reputation:
3,240
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Location:
São Paulo, Brazil
Twitter:
jarretinha
Last seen:
3 months ago
Joined:
7 years, 6 months ago
Email:
j*********@gmail.com

Former researcher at HCFMUSP, data scientist at Cargill in SP/Brazil, biologist and computer geek. Fond of genomic and genetic architecture. I think that everyone in the field should take one or two courses in populations genetics. It would help a lot...

You can find me on google things. May the effect size be with thee!

Posts by Jarretinha

<prev • 264 results • page 1 of 27 • next >
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Answer: A: Subread average running time
... Well, Wei answered my questions in the subread mail list. I think the answers are worthy here at Biostars. Of course,  I've added some of my own observations. When the value provided to '-I' option is greater than 16, subjunc (and also subread aligner) will perform read assembly to try to discover ...
written 19 months ago by Jarretinha3.2k
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Subread average running time
... I've recently updated a RNA-seq pipeline based on subread from 1.4.6 to 1.5.0-p1 on my linux server. Everything seems fine, except the running time. For the older version, it took about 2 to 3 hours to run a complete subjunc cycle (with --allJunctions) on a TruSeq human RNA-seq dataset (about 66M re ...
subjunc subread rna-seq written 20 months ago by Jarretinha3.2k
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Comment: C: GRCh38 BAM with hg38 VCFs
... These links are dead. NCBI moved the content to another folder and declared it frozen. Check this.   ...
written 20 months ago by Jarretinha3.2k
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Comment: C: Interpreting Genome_Structural_Correction Block_Bootstrap.Py
... ./block_bootstrap.py -1 ~/Downloads/upload/diff.median.g20.bed -2 ~/Downloads/upload/my_regions_shuffled.bed -d ~/Downloads/upload/hg19.extents.bed -r 0.01 -n 1000 -t cc Z Score: -0.460299602549 p-value: 0.322650593215 ...
written 3.5 years ago by Jarretinha3.2k
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Comment: C: Interpreting Genome_Structural_Correction Block_Bootstrap.Py
... Your bed files look OK. I wasn't able to reproduce your error (no my_regions_shuffled2.bed in your link). I've made one on my own. Comparing your diff file against its shuffled version using hg19.rmsk gives meaningful results for a broad range of r-values (all slightly negative Z-scores). So, everyt ...
written 3.5 years ago by Jarretinha3.2k
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Comment: C: Interpreting Genome_Structural_Correction Block_Bootstrap.Py
... Nah! I looked at the __new__ function. It expects sequence coords. Again, are you sure about your data files? No negative coords? No way too big number to be represented by a long? 'Cause now it really seems to be a bug . . . ...
written 3.5 years ago by Jarretinha3.2k
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Comment: C: Where Do I Find Genomic Coordinates For Human Cytogenetic Bands According To Ent
... Ah! I've found other utilities for this package. ...
written 3.5 years ago by Jarretinha3.2k
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Comment: C: Interpreting Genome_Structural_Correction Block_Bootstrap.Py
... It's not a dependency. But, it will use it if available. It seems that the statistical_functions.py (required by base_types.py) is running without numpy. Try to install numpy (or check if it's installed). Numpy has better numerical type support and should get rid of this error. ...
written 3.5 years ago by Jarretinha3.2k
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Comment: C: Interpreting Genome_Structural_Correction Block_Bootstrap.Py
... Are you using numpy? It looks like a numerical exception (value too big to be held by your int/long int type). Are your machine 64 bits? Can you edit your coment to put the error inside a code block? It's hard to read it like this. Maybe a pastebin link should be a better option. ...
written 3.5 years ago by Jarretinha3.2k
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Comment: C: Interpreting Genome_Structural_Correction Block_Bootstrap.Py
... You´ re using too few samples (-n 20 is just for testing). The relationship is described in the GSC draft starting at page 26. What kind of feature are you testing? ...
written 3.5 years ago by Jarretinha3.2k

Latest awards to Jarretinha

Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: What'S The Easiest Way To Blast 5000 Sequences Against An Exon Fragment?
Popular Question 16 months ago, created a question with more than 1,000 views. For What Are The Most Reliable Normalization Methods For Microarrays?
Great Question 16 months ago, created a question with more than 5,000 views. For Best Practices/Softwares To Calculate Ka/Ks Ratio
Student 16 months ago, asked a question with at least 3 up-votes. For What Are The Most Reliable Normalization Methods For Microarrays?
Scholar 19 months ago, created an answer that has been accepted. For A: Ucsc And Ncbi Cytoband Location For Human Gene Scn5A Are Different. Why?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: How To Simulate The Null Distribution For Tajima'S D?
Good Question 2.1 years ago, asked a question that was upvoted at least 5 times. For Tips To Build A Data Storage For Bioinformatics
Prophet 2.1 years ago, created a post with more than 20 followers. For Best Practices/Softwares To Calculate Ka/Ks Ratio
Appreciated 2.6 years ago, created a post with more than 5 votes. For C: Nobel Prize And Bioinformatics
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Hardware Resources For Hpc In Bioinformatics
Good Question 2.6 years ago, asked a question that was upvoted at least 5 times. For Hardware Resources For Hpc In Bioinformatics
Epic Question 2.6 years ago, created a question with more than 10,000 views. For Best Practices/Softwares To Calculate Ka/Ks Ratio
Popular Question 3.1 years ago, created a question with more than 1,000 views. For How To Generate The Set Of Sequences At A Given Edit Distance From A Reference?
Good Answer 3.1 years ago, created an answer that was upvoted at least 5 times. For A: Understanding How Snps Affect The Association Score In A Gwas
Appreciated 3.1 years ago, created a post with more than 5 votes. For C: Nobel Prize And Bioinformatics
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Problems Parsing Genbank Flatfiles Generated By Ensembl
Scholar 3.2 years ago, created an answer that has been accepted. For A: Ucsc And Ncbi Cytoband Location For Human Gene Scn5A Are Different. Why?
Appreciated 3.4 years ago, created a post with more than 5 votes. For Tips To Build A Data Storage For Bioinformatics
Great Question 3.4 years ago, created a question with more than 5,000 views. For Best Practices/Softwares To Calculate Ka/Ks Ratio
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Is There Any Useful Information To Be Gathered Analyzing The Genomes Of Differen
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Is There A Site Where Call For Papers And Conferences Are Listed In One Place?
Student 3.5 years ago, asked a question with at least 3 up-votes. For A Cvs-Ish System For Genome Annotation
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: What Phylogeny Viewing Software Do You Use?

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