Questions tagged [loop]
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Remote blastn - what is breaking my (bash) loop?
I am trying to search the NCBI non-redundant database for sequences similar to a few other (~40) sequences that I already have. So I've tried running blastn remotely, and looping through multiple ...
Mapping to assemblies in subdirectories
I am performing a bash loop one liner:. for k in */Assembly/*/*.fastq; do minimap2 -ax map-ont assembly.fasta $k > mapping.sam; echo $k; done The file hierarchy ...
Generating contrast matrix for limma in loop
I am trying to generate contrast matrix for different conditions using for loop. ...
STAR aligner multiple fastq files
I’m using STAR to align fastq files from SMART-seq2. I have raw data folder containing sub-folders with samples names the sub-folders each contain fastq file. How can I make a bash command in order ...
Error after trimming illumina adapters
I am removing illumina adapters of the NGS data with a loop. My NGS data is storage in /data/HTS_seq/. I used this function: ...
How do I set a neural network to loop multiple times and average the resulting values?
I have a script in R/RStudio which creates random datasets of binomial variables, feeds them through a neural network, and calculates their likelihood ratio statistic and deviance. I'd like the script ...
How I can push a function to act on my files
I have R code takes a vcf file returns a parsed .txt output. I have 21 vcf files in a folder I named my R code parse_vcf_alt1 function
Appending some columns from one tabular file to another
I have a list of files in which I have this information ...
How can I run a command for multiple files?
I have a bunch of .vcf files in a folder and I want to run command below on all of them but doing that one by one manually is really painful. I am seeking for a way ...
How I loop over this code
I have 139 samples; In R for each sample I run below codes for example for sample 1 ...