User: thomaskuilman

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thomaskuilman790
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Posts by thomaskuilman

<prev • 42 results • page 1 of 5 • next >
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Comment: C: Bam header editing
... Can you do something along the lines samtools view -H in.bam | awk 'BEGIN { FS = OFS = "\t"; } {if  ($1 == "@SQ") { gsub("SN:", "SN:chr", $2); print $1, $2, $3; } else print; }' | samtools reheader - in.bam > out.bam where in this case awk is used to replace chromosome names from 1, ...
written 19 months ago by thomaskuilman790
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Answer: A: RNA-seq data from human tumors in mice (PDTX)
... As a matter of fact, a colleague of mine (Oscar Krijgsman) just wrote a new tool specifically for this type of analysis. It is based on the principle of aligning the reads to both human and mouse reference genomes, and then assigning reads to human / mouse based on their alignment qualities to these ...
written 2.0 years ago by thomaskuilman790
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Comment: C: Entrez Direct to retrieve Protein and Coding sequences from NCBI accesion
... An R-based solution would be to use the `Bioconductor` package `BiomaRt`; please see my post [here][1]. Since you have the exact chromosomal position already, you can easily covert this to sequences. You can find the appropriate filters (chromosome, start and end position) using `listFilters(ensembl ...
written 2.0 years ago by thomaskuilman790
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Answer: A: What's more clear, loops or functions?
... My personal view is that using `apply` type of functions is actually the cleaner way and is also easier to read. For instance, there is no need for declaring any extra 'dummy' variables that get filled during the looping. A simple way of reading tables and assembling those into a single `data.frame` ...
written 2.0 years ago by thomaskuilman790
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Answer: A: how to deal with sra files which can generate three fastq files?
... Please see my previous [post][1]: this is due to the fact that BOTH paired and unpaired reads are included in these sra files. Using the `--split-files` option does not work since this would lead to fastq-files that are incomplete. What you did is correct; simply use the files ending with `_1` and ` ...
written 2.0 years ago by thomaskuilman790
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Comment: C: Download STRING database with Protein name
... As pointed out [here][1] and [here][2], this is likely due to a server being temporarily down. I am not sure where you are, but you can try any of these mirrors https://www.ensembl.org/ https://uswest.ensembl.org/ https://useast.ensembl.org/ https://asia.ensembl.org/ by adding the arguments `ho ...
written 2.0 years ago by thomaskuilman790
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Answer: A: Download STRING database with Protein name
... Here is an R-based solution: > test [1] "ENSP00000263431" "ENSP00000353863" "ENSP00000342026" "ENSP00000240874" > library("biomaRt") > ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") > conversion.table <- getBM(attributes = c("ensembl_peptide_i ...
written 2.0 years ago by thomaskuilman790
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Answer: A: How to calculate rooted bifurcating tree shapes
... An R implementation would be as follows: S <- NULL for (n in 1:19) { if (n == 1) { S <- 1 } else if (n%%2 == 0) { S <- c(S, sum(S[seq_len((n/2)-1)] * S[(n-1):(n-((n/2)-1))]) + S[n/2] * (S[(n/2)]+1)/2) } else { ...
written 2.0 years ago by thomaskuilman790
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Answer: A: R "object not found"
... First, it would be helpful if you provide the complete output from your console, since it will help figuring out the details of the problem. The error you mention can only arise from `dim()`: > dim(non.existing.variable) Error: object 'non.existing.variable' not found This only occurs ...
written 2.0 years ago by thomaskuilman790
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Comment: C: Merging a list of genes/features within genomic ranges
... You seem to be on the right way, and using `GRanges` would be the principled way to do this in R. It would be helpful to provide what you have tried already, and ideally a sample of the `GRanges` objects that you would like to merge (you can do that using `dput()`) ...
written 2.0 years ago by thomaskuilman790

Latest awards to thomaskuilman

Appreciated 14 months ago, created a post with more than 5 votes. For A: TCGA clinical data: stage of tumor at time biopsy was taken
Appreciated 14 months ago, created a post with more than 5 votes. For TCGA clinical data: stage of tumor at time biopsy was taken
Appreciated 14 months ago, created a post with more than 5 votes. For Plotting GSEA output in R
Great Question 14 months ago, created a question with more than 5,000 views. For Plotting GSEA output in R
Popular Question 14 months ago, created a question with more than 1,000 views. For How to extract fastq files from SRA data that contains both paired and unpaired reads
Popular Question 14 months ago, created a question with more than 1,000 views. For TCGA clinical data: stage of tumor at time biopsy was taken
Popular Question 14 months ago, created a question with more than 1,000 views. For Plotting GSEA output in R
Scholar 14 months ago, created an answer that has been accepted. For A: Clinical Data of GBM
Scholar 14 months ago, created an answer that has been accepted. For A: unsuccessful split of bam file by samtools and bamtools
Scholar 14 months ago, created an answer that has been accepted. For A: Download STRING database with Protein name
Scholar 14 months ago, created an answer that has been accepted. For A: how to deal with sra files which can generate three fastq files?
Scholar 14 months ago, created an answer that has been accepted. For A: Split columns keep the first coordinate from start and end
Scholar 14 months ago, created an answer that has been accepted. For A: TCGA clinical data: stage of tumor at time biopsy was taken
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Clinical Data of GBM
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to derive overall survival and progression free survival from TCGA clinical
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: unsuccessful split of bam file by samtools and bamtools
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Split columns keep the first coordinate from start and end
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: TCGA clinical data: stage of tumor at time biopsy was taken
Student 14 months ago, asked a question with at least 3 up-votes. For TCGA clinical data: stage of tumor at time biopsy was taken

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