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Commit d837fea2 authored by Anna Buschart's avatar Anna Buschart
Browse files

links in taxonomy text

parent 441fa0d5
......@@ -37,7 +37,7 @@ grep motus.processing -v metaT.mOTU.counts | cut -f 1 >> mOTUs.present
cat mOTUs.present | sort | uniq > mOTUs.present.all
```
With the help of the R script `getValidGenes1.R`, we then searched the mapping files _mOTU.v1.padded.motu.linkage.map_ and _mOTU.v1.map.txt_ for the genes belonging to the mOTUs found in the sample. The genes were then extracted from the marker gene collection in COG-wise fashion into a new fasta file.
With the help of the R script [`getValidGenes1.R`](getValidGenes1.), we then searched the mapping files _mOTU.v1.padded.motu.linkage.map_ and _mOTU.v1.map.txt_ for the genes belonging to the mOTUs found in the sample. The genes were then extracted from the marker gene collection in COG-wise fashion into a new fasta file.
```
for cog in `cut -f 3 ../../mOTU.v1.padded.motu.map | sort | uniq`
......@@ -70,7 +70,7 @@ do
cd ../
done
```
We then performed a blastn search for each sample using the predicted genes with this COG annotation from our assemblies. The taxonomy of this hit was again filtered from _mOTU-LG.v1.annotations.txt_, _mOTU.v1.padded.motu.linkage.map_ and _mOTU.v1.map.txt_ , this time using the script `getHitPhylogenyNew.R`.
We then performed a blastn search for each sample using the predicted genes with this COG annotation from our assemblies. The taxonomy of this hit was again filtered from _mOTU-LG.v1.annotations.txt_, _mOTU.v1.padded.motu.linkage.map_ and _mOTU.v1.map.txt_ , this time using the script [`getHitPhylogenyNew.R`](getHitPhylogenyNew.R).
```
for cog in `cut -f 3 ../../mOTU.v1.padded.motu.map | sort | uniq`
......
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