Sebastian seb-mueller
seb-mueller
/ upsetR_group_overlap.R
Created
August 23, 2018 15:45
since UpsetR doesn't report back the elements for the ploted groups this function was created to to just that. See (https://github.com/hms-dbmi/UpSetR/issues/85)
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # source of this function: https://github.com/hms-dbmi/UpSetR/issues/85#issuecomment-327900647 | |
| fromList <- function (input) { | |
| # Same as original fromList()... | |
| elements <- unique(unlist(input)) | |
| data <- unlist(lapply(input, function(x) { | |
| x <- as.vector(match(elements, x)) | |
| })) | |
| data[is.na(data)] <- as.integer(0) | |
| data[data != 0] <- as.integer(1) | |
| data <- data.frame(matrix(data, ncol = length(input), byrow = F)) |
seb-mueller
/ fastq2blast.sh
Last active
May 6, 2018 17:04
Contamination checking for fasta/fastq files
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| export BLASTDB=/data/public_data/NCBI/NCBI_all/ #and specify the db as -db nt |or -db /data/public_data/NCBI/NCBI_nt/nt | |
| export PATH=/applications/UCSC-tools/:/applications/ncbi-blast+/ncbi-blast-2.2.30+/bin/:$PATH | |
| #subsetting and converting into fasta | |
| file=sample.fq.gz | |
| filefa=${file%.fq.gz}_subset.fa | |
| n=400000 | |
| zcat $file | head -n $n > ${file%.fq.gz}_subset.fq | |
| fastqToFa ${file%.fq.gz}_subset.fq $filefa |