User: geocarvalho

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geocarvalho20
Reputation:
20
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New User
Location:
Brazil/Recife
Last seen:
1 week, 1 day ago
Joined:
9 months ago
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Posts by geocarvalho

<prev • 8 results • page 1 of 1 • next >
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Answer: A: How to start analyzing next-generation DNA and RNA sequencing data?
... As you are familiar with R, see [Harvardx](http://rafalab.github.io/pages/harvardx.html) classes. I also recommend starting reading [Biostar Handbook](https://www.biostarhandbook.com/). Nowadays, I'm migrating my shell/python pipelines to [pipeline frameworks](https://www.ncbi.nlm.nih.gov/pubmed/2 ...
written 5 weeks ago by geocarvalho20
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Answer: A: Extract Sub-Set Of Regions From Vcf File
... bedtools intersect worked better to me `intersectBed -a input.vcf -b /path/to/my.interval.bed -header > output.vcf` ...
written 8 weeks ago by geocarvalho20
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Answer: A: Extract Sub-Set Of Regions From Vcf File
... bedtools intersect worked better to me `intersectBed -a input.vcf -b /path/to/my.interval.bed -header > output.vcf` ...
written 8 weeks ago by geocarvalho20
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Comment: C: Bioinformatics Data Analyst, University of Pennsylvania, Philadelphia
... I would like to try, how can I do it? ...
written 7 months ago by geocarvalho20
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Answer: A: Where can I find a sample analysis pipeline for DNA?
... More examples of pipeline that you can extract some analysis are [SpeedSeq][1], [bcbio][2] and [IMPACT-pipeline][3]. [1]: https://github.com/hall-lab/speedseq [2]: https://github.com/chapmanb/bcbio-nextgen [3]: https://github.com/rhshah/Exome-Pipeline ...
written 7 months ago by geocarvalho20
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Answer: A: Different reference and variant allele in IonTorrent variantCaller
... I think it is a problem related to left and right-normalization to represent indels in VCF. I recommend read [this article][1] from Annovar web-site. [1]: http://annovar.openbioinformatics.org/en/latest/articles/VCF/ ...
written 7 months ago by geocarvalho20
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Answer: A: Copy Number Variation Tools
... I'm trying to study Structural Variants in Genome first, but I already noted some softwares for Exome: [cnvScan][1], [CoNIFER][2], [exomeCopy][3], [CONTRA][4], [EXCAVATOR2][5], [CODEX][6], [CLAMMS][7]. [1]: https://github.com/PubuduSaneth/cnvScan [2]: https://github.com/nkrumm/CoNIFER [3]: ...
written 8 months ago by geocarvalho20
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Answer: A: Annotation of Structural Variants and CNVs
... I'm searching something to annotate CNV in Genome, Exome and Target sequencing. For Genome the best promise to me was [ADVISER][1], but it's online and didn't work to me. For exome I think that [cnvScan][2] could work well. I tried Annovar and Vep, but I need more information. What are you using tod ...
written 8 months ago by geocarvalho20

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Supporter 7 months ago, voted at least 25 times.

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