How to run Pilon on a batch of 100 input files?
How to run Pilon on a batch of 100 input files? Is it possible using Linux Shell? Need a code examples.
pilon
batch
• 1,324 views
•
link
written
by
matveyspr •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Use part of the name of the input file in the Snakemake
written by kamanovae •I have two input files in SAMPLES folder: SRR13510812_1.fastq SRR13510812_2.fastq But I need the input files to have the following names to run the bash …
-
R with HPC
written by storm1907 •Hello, I have a custom R script, that I need to run on HPC server, not in Rstudio. I am unable to run this script; …
-
bedGraphToBigWig file converter
written by iridha •Hello All, I have MedIpP-seq replicates of same sample. I need to use plotProfile from deeptools to compare them together. for that I need to …
-
Running python script in Snakemake without input/output
written by Hansen_869 •Hi I have a very simple question. Is it possible to run a python script in a snakefile, without specifying an output/input? I have a …
-
How to visualize bam, bed and vcf files programmatically using Python and Shell or a Linux software?
written by informatics_warwick •How to visualize bam, bed, and vcf files programmatically using Python and Shell or a Linux software? Have these files coming from the NGS microbial …
-
How to submit a Pilon fasta output to the RAST annotation service using Shell or Python code?Are th…
written by bioinf_ukraine •How to submit a Pilon fasta output to the RAST annotation service using Shell or Python code? Are there any clear code examples on how …
-
Are there any working GNU parallel or similar Shell code examples on how to run Pilon, Prokka, VT a…
written by england_bioinformatics_team •Are there any working GNU parallel or similar Shell code examples on how to run Pilon, Prokka, VT and Snpeff tools on a batch of …
-
Are there any GNU parallel or similar Shell/Bash code examples on how to run Snap and BWA aligners …
written by england_bioinformatics_team •Are there any GNU parallel or similar Shell/Bash code examples on how to run Snap and BWA aligners on a batch of paired .fastq files? …
-
Is it possible to run variant calling software in parallel, are there any Shell and Python/R code e…
written by bioinform •Is it possible to run variant calling software in parallel for a 1000 of bacterial BAMs, are there any Shell and Python/R code examples available?
-
How To Run Muscle In Batch?
written by biolab<p>Hi everyone,</p> <p>I am using muscle for multi-sequence alignment. My problem is I have several thousand input files, and need to run them in batch. …
What have you tried? How do you run your program on one input file? How much shell scripting do you know?
Hello matveyspr!
We believe that this post does not fit the main topic of this site.
It is unclear what you are asking, what have you tried?
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!