User: benformatics

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benformatics160
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Posts by benformatics

<prev • 21 results • page 1 of 3 • next >
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Answer: A: get mRNAs by TxDb
... The *transcripts()* function will return coordinates for the entire range of a given transcript including introns. To get only the exonic regions use *exonsBy()* ## known exons for each transcript exonsBy(TxDb.Hsapiens.UCSC.hg38.knownGene,'tx') ## known exons for each gene exon ...
written 8 months ago by benformatics160
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Comment: C: COSMIC vcf file compatibility for Mutect2
... If anyone wants to do this in R, it a lot easier: library(VariantAnnotation) ## import cosmic vcf file cos.ens <- readVcf('./data/CosmicCodingMuts.vcf') ## check current chr names seqinfo(cos.ens) ## set UCSC compatible chromosome names seqlevelsStyle(cos.e ...
written 9 months ago by benformatics160
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Comment: C: smallRNA aligner and pipeline
... BWA Small RNA: https://www.biostars.org/p/3399/ There are a lot of small RNA profiling papers here are some examples: 1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334700/ 2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079977/ ...
written 14 months ago by benformatics160
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Answer: A: smallRNA aligner and pipeline
... Many publications involving smallRNA use standard aligners (e.g. bowtie, BWA, etc..). In general, they align their reads to the genome and then subset their alignments based on metrics such as size and whether or not they match the locations of previously annotated RNA features. The major obstacle ...
written 14 months ago by benformatics160
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Check my work? Hyper geometric test on enrichment between iCLIP sites across experiments
... Hi I was hoping for some more feedback on this test I am trying to perform to check for enrichment at specific sites throughout the genome and my statistics background isn't great. _____ Here is the current setup: Given: - genomic coordinates of iCLIP binding sites (single nucleotide position corre ...
enrichment hypergeometric written 18 months ago by benformatics160 • updated 18 months ago by michael.ante2.5k
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Answer: A: How To Get The Gene Name Interactively In A R Plot
... This is also super easy if you are already good with ggplot as [plotly][1] has added a library/function to do just this. All you need to do is make sure that your 'text' aesthetic is the text of interest. library(ggplot2) library(plotly) ## given test.df your data.frame with inter ...
written 19 months ago by benformatics160
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Answer: A: Duplicate miRNAs with different read counts in miRDeep2
... I believe this was answered previously: https://www.biostars.org/p/90159/ ...
written 20 months ago by benformatics160
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Answer: A: How Many Reads In A Bam File Are Aligned To a Specific Region
... An R code version using GenomicRanges. Not super fast but will do the job and let you keep working with the information in R. library(GenomicAlignments) library(rtracklayer) ## import bam file bamfile <- readGAlignments('sample.bam') ## assuming single end otherwise use read ...
written 20 months ago by benformatics160
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Answer: A: How to merge (or perform left joins) on GRange objects?
... I think the simplest way would be to do as you suggested and use the peakNames string. Your main problem overall however is the following: ![example case][1] You need to have a plan to address the above. And that is only a simple case you could have multiple chains like the above. Are you going ...
written 20 months ago by benformatics160
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Answer: A: Calculation of read counts in RNA-seq
... Given that they did this in R using `GenomicRanges`/`GenomicFeatures`, my assumption would be that the last section refers to the exact ranges that were used in the `summarizeOverlaps()` call. In this case they probably used their alignments (BAM files) and overlapped them with a `GRangesList` that ...
written 20 months ago by benformatics160

Latest awards to benformatics

Scholar 8 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Appreciated 9 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: ATAC-seq peak calling with MACS
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: ATAC-seq peak calling with MACS

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