Commit a339ecb7 authored by Beatriz Vicoso's avatar Beatriz Vicoso
Browse files

Update dNdS.md

parent 8071484f
......@@ -24,7 +24,9 @@ ln -s ../Barb.trinity.fasta.long.500bp_min_unwrapped.fasta .
Keep only longest ORF:
```
perl ~/scripts/GetLongestCDS_v2_October2020.pl Cyprinus_carpio-mRNA.fa
#make all capital letters
cat Cyprinus_carpio-mRNA.fa | perl -lane 'print uc($_)' > Cyprinus_carpio_capital.fa
perl ~/scripts/GetLongestCDS_v2_October2020.pl Cyprinus_carpio_capital.fa
perl ~/scripts/GetLongestCDS_v2_October2020.pl Barb.trinity.fasta.long.500bp_min_unwrapped.fasta
```
......@@ -41,3 +43,10 @@ And make three lists for the three analyses:
cat Barb_Carp_1to2_exhaust_correctChrom.txt | awk '{print $2, $5}' > List_barb_subB.txt
cat Barb_Carp_1to2_exhaust_correctChrom.txt | awk '{print $3, $5}' > List_subA_subB.txt
```
## Get dS values
```
perl dnds_estimate.pl List_barb_subA.txt Cyprinus_carpio_capital.fa.cds Cyprinus_carpio_capital.fa.cds dS_ab
```
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