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Midoux Cedric
DIGESTOMIC
Commits
8164ff5d
Commit
8164ff5d
authored
Jun 11, 2019
by
Midoux Cedric
Browse files
ghostKOALA - Update README.md
parent
83e9b06e
Changes
1
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README.md
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8164ff5d
...
...
@@ -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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