Commit 35a37fe6 authored by Beatriz Vicoso's avatar Beatriz Vicoso
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Update microsynteny.md

parent 96056ce7
......@@ -2,3 +2,19 @@
WD: /nfs/scistore03/vicosgrp/bvicoso/FishFun/Carp2022/5-MicroSynteny
## Get files
We need the location of each gene on a genomic scaffold (inferred with blat), and the scaffold-chromosome correspondence (extracted from the genome fasta file itself):
```
ln -s ../1-Trios/1-Carp_GeneSubgenome/Ccarp_RNA_vs_genome.blat.sorted.besthit .
ln -s ../1-Trios/1-Carp_GeneSubgenome/Scaffold_chromosome.joinable .
```
Let's also get the list of homeologs:
```
ln -s ../1-Trios/3-OrthoTables/Barb_Carp_1to2_exhaust_correctChrom.txt .
```
## Merge into usable table
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