User: Pablo

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Pablo1.9k
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Posts by Pablo

<prev • 114 results • page 1 of 12 • next >
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Answer: A: Issue with ExAC and 1000g hg38 lifted-over data and systematic failure of annota
... In my opinion, this sounds like a problem in the lift-over procedure, as opposed to a failure in the annotation software. In order to correctly lift-over variants (e.g. a VCF file from ExAC), not only the coordinates should be changed, but also the variant's REF and ALT fields must be complemente ...
written 2.0 years ago by Pablo1.9k
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Answer: A: Why some SNP databases don't contain the strand information
...   It depends in which format you retrieve the database. For instance, ClinVar is available in VCF and by definition VCF represents variants ok the plus strand, so there is no need to specify the strand (it is implied by the file format). For what you are trying to achieve you don't need any of tha ...
written 3.8 years ago by Pablo1.9k
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Comment: C: snpEff suitable for Bathycoccus prasinos?
... I'm not sure what you mean by " heard some whispers recently saying that this tool wasn't up to date", but I'm developing SnpEff and the latest release was just a couple of days ago (and there have been new versions being released every couple of months since its inception). The categories, which a ...
written 4.0 years ago by Pablo1.9k
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Answer: A: Variant annotation: Multiple values in some fields like SIFT_Pred
... dbNSFP provides multiple values for those scores and SnpEff simply annotates them all. The reason dbNSFP provides different values is related to how each score is calculated. For instance the number of PolyPhen entries usually  the same as the number of Uniprot IDs, similarly the number of SIFT ent ...
written 4.0 years ago by Pablo1.9k
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Answer: A: Which GRCh37 version to use from snpEff databases for BAMs mapped with GRCh37-li
...   GRCh37.XX are form ENSEMBL genes. I'd recommend you use the latest one available (GRCh37.75).   ...
written 4.1 years ago by Pablo1.9k
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Answer: A: Freebayes and snpeff give different number of SNPs
... If a VCF entry has two (or more) alts, SnpEff counts it as two (or more) SNPs.  For instance     CHR:1, POS:1234, REF:A, ALT:C is 1 SNP (A>C) , whereas this entry     CHR:1, POS:1234, REF:A, ALT:C,G is counted as 2 SNPs (A>C and A>G).  I don't know how freebayes counts, but I'm assumi ...
written 4.4 years ago by Pablo1.9k
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Comment: A: Configurattion for RNAseq analysis and Genome annotation and assembled of Eukari
...   If you are asking about programs and methods, a good starting point is "GATK's best practices": https://www.broadinstitute.org/gatk/guide/best-practices   ...
written 4.5 years ago by Pablo1.9k
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Comment: C: Prediction of the functional effect of nsSNPs
... OK, my bad then. I'll try to delete  / edit this answer.   ...
written 4.5 years ago by Pablo1.9k
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Comment: C: Mission Impossible: you have 1 minute to analyze the Ebola Genome
... It's weird that they mention KM034562 in the main paper, they asked me to provide "KJ660346" for their analysis... ...
written 4.5 years ago by Pablo1.9k
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Comment: C: Prediction of the functional effect of nsSNPs
... Indeed. The question mentions "protein SNP analysis", so I'm assuming these are from sequencing data (otherwise it would be something like "protein polymorphism analysis"). May be sana can clarify a little bit more in the formats being used for the analysis...   ...
written 4.5 years ago by Pablo1.9k

Latest awards to Pablo

Great Question 3.7 years ago, created a question with more than 5,000 views. For Bowtie Pair-End Broken?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Bowtie Pair-End Broken?
Commentator 3.7 years ago, created a comment with at least 3 up-votes. For C: Confusion with High Confidence SNP Calls (Overlap B/w RNA-seq & WGBS calls) and
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Define If Chip Peaks Are Located In Exon, Intron, Promoter, 3Prime Utr
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Coverage For De Novo Snp Detection In Microbes?
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Fast Qseq To Fastq Converter
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: Define If Chip Peaks Are Located In Exon, Intron, Promoter, 3Prime Utr
Scholar 4.0 years ago, created an answer that has been accepted. For A: Prediction of the functional effect of nsSNPs
Scholar 4.4 years ago, created an answer that has been accepted. For A: Prediction of the functional effect of nsSNPs
Teacher 4.4 years ago, created an answer with at least 3 up-votes. For A: Define If Chip Peaks Are Located In Exon, Intron, Promoter, 3Prime Utr
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Define If Chip Peaks Are Located In Exon, Intron, Promoter, 3Prime Utr
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: Compare Two Fasta Files By Headers
Centurion 4.5 years ago, created 100 posts.
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Popular Question 4.7 years ago, created a question with more than 1,000 views. For How Bimodal Is A Methylation Distribution?
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Bowtie Pair-End Broken?
Guru 5.1 years ago, received more than 100 upvotes.
Teacher 7.0 years ago, created an answer with at least 3 up-votes. For A: Define If Chip Peaks Are Located In Exon, Intron, Promoter, 3Prime Utr
Teacher 7.2 years ago, created an answer with at least 3 up-votes. For A: Joining Snpeff And Vcf
Teacher 7.4 years ago, created an answer with at least 3 up-votes. For A: How To Extract Random Snps From Whole Genome Data?
Teacher 7.7 years ago, created an answer with at least 3 up-votes. For A: Coverage For De Novo Snp Detection In Microbes?
Teacher 7.8 years ago, created an answer with at least 3 up-votes. For A: Are Chip-Seq Replicate Data Used As Controls ?
Good Answer 7.9 years ago, created an answer that was upvoted at least 5 times. For A: Compare Two Fasta Files By Headers
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Teacher 7.9 years ago, created an answer with at least 3 up-votes. For A: Compare Two Fasta Files By Headers

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