Commit df08d6e2 authored by Noort, Maite van den's avatar Noort, Maite van den
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Update commands_commandline.md

parent 80eeb99d
[Fig1]: ./Pictures/Internship-Maite-epiGBS2/MicrosoftTeams-image__2_.png "library(ggpubr)"
# Handy commands
## Making a new file
Making a new file named barcode_inforamtion.txt with the lines 10 to 100 from a big file named process_radtags.clone.log
`sed -n -e '10,100p' process_radtags.clone.log > barcode_inforamtion.txt`
## Merging files together
Merging files together by appending one file under the other. And creating a new file with the two files in it:
`cat file1.txt file2.txt > newbigfile1plus2.txt`
## Check for silly characters
To check files for silly charaters you don't want in your file you can use the following command:
`cat -A filename`
You can also remove those characters with the following command:
`dos2unix filename`
## Showing only a few lines of a zipped file
If you want to show only a few lines of a zipped file without oped the whole fil use this command:
`zcat filename | sed -n 'regeln;regeln;einderegelq'`
## Making links
To link files to other directories without copieing the whole file:
`ln -s "path to my files" "path to link, where I want them"`
# All commands that are excuted in the commandline
## Error pipeline library(ggpubr)
The error prevented the report.md from being completed.
The error was about the R library `ggpubr`
......@@ -8,13 +29,3 @@ Excuted commands:
`conda activate /mnt/nfs/bioinfdata/home/NIOO/maiten/duckweed_epiGBS/lane2_denovo8/epigbs2/.snakemake/conda/7d295ce0`
`R`
When you have completed this, you will enter an R environment, where you can perform R.
![][Fig1]
## Making a new file
Making a new file named barcode_inforamtion.txt with the lines 10 to 100 from a big file named process_radtags.clone.log
`sed -n -e '10,100p' process_radtags.clone.log > barcode_inforamtion.txt`
## Merging files together
As we mentioned earlier, there is also a way append files to the end of an existing file. Type the cat command followed by the file or files you want to add to the end of an existing file. Then, type two output redirection symbols (>>) followed by the name of the existing file you want to add to.
`cat file5.txt >> file4.txt`
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