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| − | Successful tiny examples.
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| | ==In bash, at Moria== | | ==In bash, at Moria== |
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| | Extract the first column: | | Extract the first column: |
| | awk '{print $1}' sizes.out > sizesQ.out | | awk '{print $1}' sizes.out > sizesQ.out |
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| − | Get the lengths of the reads of a fastq file (after [http://onetipperday.sterding.com/2012/05/simple-way-to-get-reads-length.html this]):
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| − | cat /Users/Moria/Desktop/g043.refined.1.fq | awk '{if(NR%4==2) print length($1)}' > /Users/Moria/Desktop/g043.refined.1.EXTRACT.fq
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| | ==At CUBE== | | ==At CUBE== |
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| | for file in /proj/genomes/Thiobios/data/ThiobiosMAGs/* ; do gc $file >> gc.out ; done | | for file in /proj/genomes/Thiobios/data/ThiobiosMAGs/* ; do gc $file >> gc.out ; done |
| | awk '{print $4}' gc.out > gcQ.out | | awk '{print $4}' gc.out > gcQ.out |
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| − | Assess completeness, contamination and heterogeneity of the genomes in a folder:
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| − | 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
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| − | Check for tRNAs of the genomes in a folder:
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| − | cd /proj/genomes/Thiobios/data/ThiobiosMAGs
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| − | for file in ./* ; do tRNAscan-SE -B $file -o /proj/genomes/Thiobios/results/2017_08_25_tRNAscan-SE/$file.tRNAscan-SE.out ; done
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| − | ==With R (and RStudio)==
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| − | Extract a part of a sequence, using ''ape'':
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| − | s2c(c2s(as.matrix(g43Z2[1])[44214:47213]))
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| − | Build a Maximum Likelihood tree, using ''ape'' and ''phangorn'':
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| − | ali.16SB<-as.phyDat(ssuAlignB[c(2:10,1),segSitB])
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| − | dist.16SB<-dist.ml(ali.16SB)
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| − | tree.16S.njB<-root(NJ(dist.16SB),10)
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| − | mod.16SB<-modelTest(ali.16SB,model="all",multicore=TRUE)
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| − | env.16SB<-attr(mod.16SB,"env")
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| − | fitStart.16SB<-eval(get(mod.16SB$Model[which.min(mod.16SB$BIC)],env.16SB),env.16SB) # mod.16SB$Model[which.min(mod.16SB$BIC)]="K80"
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| − | fitNJ.16SB<-pml(tree.16S.njB,ali.16SB)
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| − | fit.16SB<-optim.pml(fitNJ.16SB,rearrangement="stochastic",model="K80",optInv=FALSE,optGamma=FALSE)
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| − | bs.16SB<-bootstrap.pml(fit.16SB,bs=1000,optNni=TRUE,multicore=TRUE)
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| − | plotBS(fit.16SB$tree,bs.16SB,p=50,type="p",bs.adj=c(1.2,-.7))
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| − | add.scale.bar()
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