Moderator: Kevin Blighe

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Kevin Blighe37k
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'Incrocio le dita e spero'

'There are mountains in our way... but we climb a step every day'

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Developer / Maintainer of Bioconductor packages:

Posts by Kevin Blighe

<prev • 5,345 results • page 2 of 535 • next >
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Comment: C: Too low FPKM values from StringTie
... Hey, if you just follow the recommendation by shawn (Salmon --> DESeq2), then you'll have data that is suitable for differential expression. Salmon will require input FASTQ files, I believe, and bypasses the production of a BAM file. The other method, STAR --> HTSeq --> DESeq2, will produc ...
written 1 day ago by Kevin Blighe37k
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Comment: C: junction_annotation.py: How many 'novel' splice junctions/splice events are reso
... Double-check the version that you are using. Note the release notes: RSeQC v2.6.1 Fix bug in “junction_annotation.py” in that it would report some “novel splice junctions” that don’t exist in the BAM files. This happened when reads were clipped and spliced mapped simultaneously. *[source: h ...
written 1 day ago by Kevin Blighe37k
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Comment: C: Determining the presence of alleles based on depth, coverage, divergence, MAF
... I am not familiar with the program, however, the default for depth appears to be 5: --min_depth MIN_DEPTH Minimum mean depth to flag as dubious allele call (default 5) Taken from: https://github.com/katholt/srst2 ...
written 1 day ago by Kevin Blighe37k
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Comment: C: Too low FPKM values from StringTie
... All RNA-seq count data is shifted toward zero, so, that is expected. RNA-seq counts follow a negative binomial distribution. I don't believe that production of FPKM expression values results in an overall change from this data distribution. A transformation of normalised counts via, e.g., variance-s ...
written 1 day ago by Kevin Blighe37k
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Comment: C: HMM and NGS mapping
... Can you elaborate on what you mean by the 'reference transcript HMM profiles'? ...
written 1 day ago by Kevin Blighe37k
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Answer: A: Accessing population specific mutation data from 1000 genome.
... Yes, you would mainly want the following EUR populations, i.e.: - CEU, Utah Residents (CEPH) with Northern and Western European Ancestry - TSI, Toscani in Italia - GBR, British in England and Scotland The others are: - FIN, Finnish in Finland - IBS, Iberian Population in Spain People fro ...
written 1 day ago by Kevin Blighe37k
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Comment: C: Population Private SNPs
... ^^ It does indeed seem to be as straight forward as how zx8754 describes. The allele frequency data can be used to infer alleles that are only present in one population group or another. If I was actively working on this, I would spend some time to get the 1000 Genomes data into a single BCF and als ...
written 1 day ago by Kevin Blighe37k
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Comment: C: GOplot and making circle_dat out of microarray and DAVID data
... Looks like your data has '*Category*' whereas the function looks for '*category*' (small 'c'). You should also look into your objects to see how they look. It is a good habit to have. For example: head(genelist) head(david) As a side note, I posted a tutorial for plotting DAVID results: h ...
written 1 day ago by Kevin Blighe37k
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Comment: C: Comparison of variant distribution between chromosomes
... Yes, to further elaborate on Erin's final point, as an example, recent *in silico* prediction tools have compared mutation frequencies against random mutation backgrounds and/or 'derived' alleles that have become fixed (conserved) in the human lineage when compared to our recent ape ancestor. If you ...
written 1 day ago by Kevin Blighe37k
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Answer: A: automatically create index files from output in bcftools
... I think that you need to clear up what your file extensions mean. With your first command, you have specified: -O b -o $x.multiallelicIndelsRemoved.1240positions.vcf.bgz `-O b` does not output a bgzipped VCF file, as your output filename (*$x.multiallelicIndelsRemoved.1240positions.vcf.bgz*) ...
written 1 day ago by Kevin Blighe37k • updated 1 day ago by WouterDeCoster36k

Latest awards to Kevin Blighe

Scholar 1 day ago, created an answer that has been accepted. For A: What is the common method(s) to detect eRNAs by using RNA-seq data?
Scholar 3 days ago, created an answer that has been accepted. For A: What is the common method(s) to detect eRNAs by using RNA-seq data?
Appreciated 3 days ago, created a post with more than 5 votes. For A: Batch effects : ComBat or removebatcheffects (limma package) ?
Popular Question 5 days ago, created a question with more than 1,000 views. For Determine % of reference genome covered by aligned SAM/BAM
Scholar 8 days ago, created an answer that has been accepted. For A: What is the common method(s) to detect eRNAs by using RNA-seq data?
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: Batch effects : ComBat or removebatcheffects (limma package) ?
Appreciated 9 days ago, created a post with more than 5 votes. For A: Batch effects : ComBat or removebatcheffects (limma package) ?
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Batch effects : ComBat or removebatcheffects (limma package) ?
Appreciated 9 days ago, created a post with more than 5 votes. For R functions for parallel processing
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Commentator 11 days ago, created a comment with at least 3 up-votes. For C: PCA in a RNA seq analysis
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: Batch effects : ComBat or removebatcheffects (limma package) ?
Scholar 14 days ago, created an answer that has been accepted. For A: What is the common method(s) to detect eRNAs by using RNA-seq data?
Scholar 17 days ago, created an answer that has been accepted. For A: What is the common method(s) to detect eRNAs by using RNA-seq data?
Teacher 17 days ago, created an answer with at least 3 up-votes. For A: Batch effects : ComBat or removebatcheffects (limma package) ?
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Commentator 18 days ago, created a comment with at least 3 up-votes. For C: bash and awk code
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Scholar 22 days ago, created an answer that has been accepted. For A: What is the common method(s) to detect eRNAs by using RNA-seq data?
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Scholar 24 days ago, created an answer that has been accepted. For A: What is the common method(s) to detect eRNAs by using RNA-seq data?

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