Difference between revisions of "HowTo"

Revision as of 23:21, 5 May 2018

Successful tiny examples.

In bash, at Moria

Generate the md5 signatures of the files in a folder:

for file in /Volumes/MBL21/A_TREASURY/012_A_TRASURY_ThiobiosGenomes/* ; do  md5 -q $file >> resultsQ.out ; done

Generate the sizes of the files in a folder:

for file in /Volumes/MBL21/A_TREASURY/012_A_TRASURY_ThiobiosGenomes/* ; do  wc -c $file >> sizes.out ; done

Extract the first column:

awk '{print $1}' sizes.out > sizesQ.out

At CUBE

GC contents of the files in a folder:

for file in /proj/genomes/Thiobios/data/ThiobiosMAGs/* ; do  gc  $file >> gc.out ; done
awk '{print $4}' gc.out > gcQ.out

Assess completeness, contamination and heterogeneity of the genomes in a folder:

checkm lineage_wf -t 8 /proj/genomes/Thiobios/results/2017_08_24_checkM/data /proj/genomes/Thiobios/results/2017_08_24_checkM/therest.checkm --tab_table --file therest.checkm.out

Check for tRNAs of the genomes in a folder:

cd /proj/genomes/Thiobios/data/ThiobiosMAGs
for file in ./* ; do tRNAscan-SE -B $file -o /proj/genomes/Thiobios/results/2017_08_25_tRNAscan-SE/$file.tRNAscan-SE.out ; done

With R (and RStudio)

extract a part of a sequence, using ape:

s2c(c2s(as.matrix(g43Z2[1])[44214:47213]))