Difference between revisions of "HowTo"
From salvaEwiki
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Assess completeness, contamination and heterogeneity of the genomes in a folder: | 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 | 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 |
Revision as of 01:36, 26 August 2017
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