User: igor

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igor3.6k
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Posts by igor

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Answer: A: best STAR options for miRNA mapping?
... Most RNA-seq tools aren't really designed for very short sequences that you get from small RNA-seq. You should look into miRNA-specific tools, such as: - miRge - http://atlas.pathology.jhu.edu/baras/miRge.html - miRDeep2 - https://www.mdc-berlin.de/8551903/en/ - miRExpress - http://mirexpress.mb ...
written 2 days ago by igor3.6k
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Comment: C: vcftools installation: vcftools/bin folder not created
... If you already have Homebrew, it might be easier to just use Homebrew Science. brew tap homebrew/science brew install vcftools See: https://github.com/Homebrew/homebrew-science ...
written 3 days ago by igor3.6k
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TCGA/GDC FPKM vs FPKM-UQ
... GDC provides RNA-seq quantification in multiple forms: > For mRNA-Seq data, the GDC generates gene level and exon level > quantification in Fragments Per Kilobase of transcript per Million > mapped reads (FPKM). To facilitate cross-sample comparison and > differential expression analysi ...
gdc rna-seq written 3 days ago by igor3.6k
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Answer: A: Benchmarking for comparing diffent variant callers
... There are a few public reference genomes listed here: http://googlegenomics.readthedocs.io/en/latest/use_cases/discover_public_data/genomic_data_toc.html ...
written 8 days ago by igor3.6k
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Answer: A: Deciding on a Variant Caller
... Different variant callers will perform differently for different samples. You have to find one that works best for yours. This means calling variants with different callers and checking which ones can be successfully validated. It sounds like you are basing your assessment based on tumor purity alo ...
written 10 days ago by igor3.6k
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Comment: C: Deciding on a Variant Caller
... Of course, that is a paper from the MuSE developers. Every variant caller that gets published claims to be better than all the previous ones. ...
written 10 days ago by igor3.6k
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Comment: C: Bioinformatics software distribution
... GitHub provides some statistics, but those are only for visitors. You can have your software tool ping a specific URL every time it is run. That's a little bit questionable from a privacy perspective, but is technically possible. For example, GATK used to have a "phone home" feature until recently ...
written 13 days ago by igor3.6k
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Comment: C: Bioinformatics software distribution
... Yes, the "releases" is not obvious at all. You can have a link in your README to the releases page, though. I think that's how I originally found out about it. ...
written 13 days ago by igor3.6k
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Comment: C: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
... If you email GEO, they can link SRA and GEO entries. Or at least they used to. ...
written 13 days ago by igor3.6k
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Comment: C: How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
... Yes, but that part is automated, so you don't have to worry about that as a submitter. ...
written 13 days ago by igor3.6k

Latest awards to igor

Teacher 5 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 8 days ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 13 days ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: (SIFT, Polyphen, PROVEAN) vs. (ANNOVAR) vs. (LOFTEE)
Scholar 5 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Student 6 weeks ago, asked a question with at least 3 up-votes. For Using PhiX to estimate bisulfite conversion rate
Scholar 6 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Best way to perform single-cell RNA-seq normalization
Scholar 12 weeks ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
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Good Question 3 months ago, asked a question that was upvoted at least 5 times. For ATAC-seq peak calling with MACS
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: read length of sequence
Scholar 4 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Popular Question 4 months ago, created a question with more than 1,000 views. For Faster BLAST alternative
Popular Question 4 months ago, created a question with more than 1,000 views. For Faster BLAST alternative
Appreciated 4 months ago, created a post with more than 5 votes. For A: Must know algorithms before attending a bioinformatics interview
Scholar 5 months ago, created an answer that has been accepted. For A: Pre-processing MiSeq Paired End data
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: How detrimental are duplicate reads in RNAseq experiments?

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