Commit 8164ff5d authored by Midoux Cedric's avatar Midoux Cedric
Browse files

ghostKOALA - Update README.md

parent 83e9b06e
......@@ -11,4 +11,46 @@ ln -s ~/DIGESTOMIC/DATA/DIGESTOMIC_J80_A_26_11_15_S1_all_R1_001.fastq.gz DATA/ra
ln -s ~/DIGESTOMIC/DATA/DIGESTOMIC_J80_A_26_11_15_S1_all_R2_001.fastq.gz DATA/raw/J80_A_R2.fastq.gz
ln -s ~/DIGESTOMIC/DATA/DIGESTOMIC_J80_B_26_11_15_S2_all_R1_001.fastq.gz DATA/raw/J80_B_R1.fastq.gz
ln -s ~/DIGESTOMIC/DATA/DIGESTOMIC_J80_B_26_11_15_S2_all_R2_001.fastq.gz DATA/raw/J80_B_R2.fastq.gz
```
\ No newline at end of file
```
## ghostKOALA
### Submit analysis
```bash
awk 'NR<=2000000' work/FGS/coassembly_FGS.faa > work/FGS/coassembly_FGS-1.faa
awk 'NR>=2000001&&NR<=4000000' work/FGS/coassembly_FGS.faa > work/FGS/coassembly_FGS-2.faa
awk 'NR>=4000001&&NR<=6000000' work/FGS/coassembly_FGS.faa > work/FGS/coassembly_FGS-3.faa
awk 'NR>=6000001&&NR<=8000000' work/FGS/coassembly_FGS.faa > work/FGS/coassembly_FGS-4.faa
awk 'NR>=8000001&&NR<=10000000' work/FGS/coassembly_FGS.faa > work/FGS/coassembly_FGS-5.faa
awk 'NR>=10000001' work/FGS/coassembly_FGS.faa > work/FGS/coassembly_FGS-6.faa
```
* Download files
* Upload on [GhostKOALA webserver](https://www.kegg.jp/ghostkoala/) with `genus_prokaryotes + family_eukaryotes + viruses ` database option
* Submit
* Download from webserver and group in order annotation files `user_ko.txt`
* Join with other tables
### KEGG orthology table
[source](http://merenlab.org/2018/01/17/importing-ghostkoala-annotations/)
```bash
cd work/ghostKOALA
wget 'https://www.genome.jp/kegg-bin/download_htext?htext=ko00001&format=htext&filedir=' -O ko00001.keg
kegfile="ko00001.keg"
while read -r prefix content
do
case "$prefix" in A) col1="$content";; \
B) col2="$content" ;; \
C) col3="$content";; \
D) echo -e "$col1\t$col2\t$col3\t$content";;
esac
done < <(sed '/^[#!+]/d;s/<[^>]*>//g;s/^./& /' < "$kegfile") > KO_Orthology_ko00001.txt
rm ko00001.keg
```
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