Commit b042b0c3 authored by Beatriz Vicoso's avatar Beatriz Vicoso
Browse files

Update BarbCarpSynteny.md

parent be58c72d
......@@ -42,4 +42,18 @@ perl ~/2-besthitblat.pl barbrna_vs_barbgenome.blat.sorted
```
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 | awk '{print $2, $3}' | grep -v 'S[0-9]*' | sort | uniq -c | sort -rn | awk '{print $2, $3, $1}' > CarpChr_BarbChr_counts.txt
```
Gives a table of counts that looks like:
CarpChr | PtetrazonaChr | GeneCount
--- | --- | ---
B7 | B7 | 341
B5 | B5 | 333
B3 | B3 | 309
B16 | B16 | 301
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