Questions tagged [loop]
The loop tag has no usage guidance.
11 questions
3
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1
answer
81
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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/...
- 61
3
votes
2
answers
522
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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 ...
- 1,027
2
votes
2
answers
159
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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 ...
- 21
2
votes
1
answer
568
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Generating contrast matrix for limma in loop
I am trying to generate contrast matrix for different conditions using for loop.
...
- 347
1
vote
1
answer
2k
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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 ...
2
votes
2
answers
81
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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:
...
- 79
1
vote
1
answer
470
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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 ...
- 129
0
votes
3
answers
115
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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
user3962
-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
...
- 2,232
2
votes
2
answers
171
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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 ...
user6517
2
votes
1
answer
214
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How I loop over this code
I have 139 samples; In R for each sample I run below codes
for example for sample 1
...
- 2,232