Commit 884a96c9 authored by Beatriz Vicoso's avatar Beatriz Vicoso
Browse files

Update BarbCarpSynteny.md

parent b042b0c3
......@@ -40,9 +40,16 @@ perl ~/2-besthitblat.pl barbrna_vs_barbgenome.blat.sorted
## Merge all files
We select carp homeologs for which the barb homolog mapped to a P. tetrazona chromosome (i.e. we filter out unmapped scaffolds).
```
cat barbrna_vs_barbgenome.blat.sorted.besthit | awk '{print $14, $10}' | sort | join /dev/stdin Ptetra_scaf_chr.joinable | awk '{print $2, $3}' | sort > PuntiusRNA_PtetraChrom.joinable
cat Barb_Carp_1to2_stringent_correctChrom.txt | awk '{print $2, $6}' | sort | join /dev/stdin PuntiusRNA_PtetraChrom.joinable | grep -v 'S[0-9]*' > PuntiusRNA_carpChr_PtetraChr.txt
```
We can also have a quick look at counts:
```
cat Barb_Carp_1to2_stringent_correctChrom.txt | awk '{print $2, $6}' | sort | join /dev/stdin PuntiusRNA_PtetraChrom.joinable | awk '{print $2, $3}' | grep -v 'S[0-9]*' | sort | uniq -c | sort -rn | awk '{print $2, $3, $1}' > CarpChr_BarbChr_counts.txt
```
......@@ -55,5 +62,8 @@ B5 | B5 | 333
B3 | B3 | 309
B16 | B16 | 301
--> 5684/5833 genes (97%) are assigned to the same chromosomal element.
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