User: benformatics

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benformatics890
Reputation:
890
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Trusted
Location:
ETH Zurich
Last seen:
6 hours ago
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3 years, 4 months ago
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Posts by benformatics

<prev • 85 results • page 1 of 9 • next >
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Answer: A: Numeric genotype to letters
... I have no idea what the format of your object is but here is a potential solution in R. Assuming you have your input file in R and it looks as follows (you can use `read.delim()`): X.CHROM START ID Ref Alt X108 X139 X159 X265 X350 1 5 5571 snp_5_5571 C T 0 0 ...
written 5 days ago by benformatics890
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Comment: C: How to subset ExpressionSet based on vector of sample names
... Does: eset_forHCC= exprs(expset_forall)[,sampleNames(expset_forall) %in% names_HCC] not work? ...
written 18 days ago by benformatics890
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Answer: A: How to randomly subset a specific number of sequences from a large fastq file?
... Please **use the search function** before posting a question. - [Question: Take A Subset Of A Fastq Paired-End Sample][1] - [Question: Extracting randomly subset of fastq reads from a huge file][2] - [Question: Selecting Random Pairs From Fastq?][3] - [Question: How to subset reads from fastq f ...
written 20 days ago by benformatics890
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Comment: C: No color observed in Colour Key of HeatMap.2
... Perhaps provide an example with a more complete dataset? Many of your objects (e.g. MTB*) were not included - so we cannot say for sure whether this is a problem that is specifically happening to you or if it is reproducible for others. ...
written 26 days ago by benformatics890
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Comment: C: About GATK data-preprocessing workflow
... Yes those are examples of metadata... but the issue here is that you are excluding the core of your data (i.e. nucleotide sequence) because of an underlying aspect of the bwa software. This is completely independent of any meta-deta. ...
written 27 days ago by benformatics890
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Answer: A: About GATK data-preprocessing workflow
... The metadata is not related to the read groups. As the skywarrior person said in the post you linked: > BWA hardclips reads if there is a significant discordance between the > best matching kmer and the read. These hardclips may end up costing > you a particular structural variant or a tr ...
written 27 days ago by benformatics890
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Answer: A: VCF INFO interpretation
... I believe all the information should be available in the [VCF format specification][1] document (click on the most recent VCF file on the left-hand column) - at least for all standard INFO fields. It sounds like you might be using freebayes so maybe check out their [pre-print][2]. You could also c ...
written 27 days ago by benformatics890
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Answer: A: Label selected genes in volcano plot from ggplot
... Your labels are of class **factor** and not **character.** If you wrap it with `as.character` in your plotting call it should work. ggplot(results) + geom_point(aes(Fold, -log10(FDR),col=sig))+ geom_text_repel(aes(Fold, -log10(FDR)),label = ifelse(results$genelabels == TRUE, as.character(result ...
written 4 weeks ago by benformatics890
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Comment: C: DEXseq Error - SummarizedExperiment
... I assume you checked that your count table actually contains non-zero counts? Ultimately, this should only provide some meta-data to the final object... the counts should remain unchanged. ...
written 4 weeks ago by benformatics890
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Comment: C: How to group gene dataset and run t.test for each row for every gene in R?
... If you are getting this data from raw RNA-Seq data your best bet is to use a well established method like [DESeq2][1] or [edgeR][2] or [limma][3]. [1]: https://bioconductor.org/packages/release/bioc/html/DESeq2.html [2]: https://bioconductor.org/packages/release/bioc/html/edgeR.html [3]: htt ...
written 4 weeks ago by benformatics890

Latest awards to benformatics

Scholar 4 weeks ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 5 weeks ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Subset of genes with at least 1 intron larger than 5000 kbp
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Appreciated 3 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Scholar 3 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Scholar 3 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
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Scholar 3 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Creating bins based on scaffold size file
Scholar 6 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: ATAC-seq peak calling with MACS
Scholar 9 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Scholar 9 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: ATAC-seq peak calling with MACS
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: ATAC-seq peak calling with MACS
Scholar 22 months ago, created an answer that has been accepted. For A: get mRNAs by TxDb
Appreciated 22 months ago, created a post with more than 5 votes. For A: ATAC-seq peak calling with MACS
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: ATAC-seq peak calling with MACS
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: ATAC-seq peak calling with MACS

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