-
Notifications
You must be signed in to change notification settings - Fork 0
Expand file tree
/
Copy pathREADME
More file actions
20 lines (14 loc) · 2.33 KB
/
README
File metadata and controls
20 lines (14 loc) · 2.33 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
USAGE
# STEP 1: clean the raw db files (only before creating the db on mascot server)
ruby scripts/clean_files.rb data/mrnas_ucsc_lineformat.txt data/proteins_ucsc_db.fa data/danRer7.fa results/mrnas_ucsc_lineformat_clean.txt results/proteins_ucsc_db_clean.fa
# STEP 2: find unannotated proteins
# ruby scripts/find_unannotated_proteins.rb results/mrnas_ucsc_lineformat_clean.txt data/1d-30oct-zfish-ucsc-db.dat results/proteins_ucsc_db_clean.fa data/junctions_high-quality.bed data/danRer7.fa results/1d-30oct/peptides-1d-30oct.bed results/1d-30oct/mrnas_unannotated.bed results/1d-30oct/mrnas_unannotated_seqs.fa results/1d-30oct/mrnas_unannotated_lineformat.txt results/1d-30oct/proteins_unannotated.fa
# ruby scripts/find_unannotated_proteins.rb results/mrnas_ucsc_lineformat_clean_.txt data/1d-16dec-zfish-ucsc-db.dat results/proteins_ucsc_db_clean_.fa data/junctions_high-quality.bed data/danRer7.fa results/1d-16dec_/peptides-1d-16dec_.bed results/1d-16dec_/mrnas_unannotated_.bed results/1d-16dec_/mrnas_unannotated_seqs_.fa results/1d-16dec_/mrnas_unannotated_lineformat_.txt results/1d-16dec_/proteins_unannotated_.fa
# STEP 3: (after running mascot for unannotated) create bed file with the peptides of the unannotated proteins
ruby scripts/peptides_to_bed.rb results/1d-30oct/mrnas_unannotated_lineformat.txt data/1d-30oct-zfish-unannotated-db.dat results/1d-30oct/proteins_unannotated.fa results/1d-30oct/peptides_on_unannotated_proteins-1d-30oct.bed
# STEP 4: (only before creating the db on mascot server) join the db files (mrnas_lineformat and proteins)
cat results/mrnas_ucsc_lineformat_clean.txt > results/mrnas_full_db_lineformat.txt
grep -v "#" results/mrnas_unannotated_lineformat.txt >> results/mrnas_full_db_lineformat.txt
cat results/proteins_ucsc_db_clean.fa results/proteins_unannotated.fa >> results/proteins_full_db.fa
# STEP 5: (after running mascot for joined) find unexplained peptides with evidence
ruby scripts/find_unexplained_peptides.rb data/1d-30oct-zfish-full-db.dat results/mrnas_full_db_lineformat.txt data/mrnas_ucsc_lineformat.txt results/1d-30oct/unexplained_peptides_of_unannotated_proteins-1d-30oct.bed results/1d-30oct/unique_peptides_of_unannotated_proteins-1d-30oct.bed results/1d-30oct/nonunique_peptides_of_unannotated_proteins-1d-30oct.bed results/1d-30oct/unexplained_peptides_of_unannotated_proteins_per_spectra-1d-30oct.bed