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Questions tagged [loop]

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3 votes
2 answers
523 views

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 ...
Laura's user avatar
  • 1,027
3 votes
1 answer
81 views

RNA-seq QC and alignment error in script

I am analyzing bulk RNA-seq data for Paired-End. I have separate scripts for fastqc, STAR & qualimap but want to run them in a single script which looks like this USAGE: sh rna-qc.sh <path/to/...
S_Malik's user avatar
  • 61
2 votes
2 answers
171 views

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 ...
user avatar
2 votes
1 answer
214 views

How I loop over this code

I have 139 samples; In R for each sample I run below codes for example for sample 1 ...
Zizogolu's user avatar
  • 2,232
2 votes
2 answers
159 views

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 ...
matt's user avatar
  • 21
2 votes
1 answer
568 views

Generating contrast matrix for limma in loop

I am trying to generate contrast matrix for different conditions using for loop. ...
user98059's user avatar
  • 347
2 votes
2 answers
81 views

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: ...
Adrián P.L.'s user avatar
1 vote
1 answer
2k views

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 ...
mobasher barsi's user avatar
1 vote
1 answer
470 views

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 ...
Equinox's user avatar
  • 129
0 votes
3 answers
115 views

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
user avatar
-1 votes
1 answer
38 views

Appending some columns from one tabular file to another

I have a list of files in which I have this information ...
Zizogolu's user avatar
  • 2,232