Sebastian seb-mueller
seb-mueller
/ fastq2blast.sh
Last active
May 6, 2018 17:04
Contamination checking for fasta/fastq files
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| 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 |
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)
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| # 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)) |