Step 23: Access to files to test all programs and scripts

If something goes wrong you can check all programs and scripts with the data files from this web page. All programs and scripts described previously have been successfully tested with files listed below.

Lycopersicon_esculentum.fasta.orig (fasta header before modifications, step 3)
Lycopersicon_esculentum.fasta (fasta header after modifications, step 3)
Lycopersicon_hirsutum.fasta.orig (fasta header before modifications, step 3)
Lycopersicon_hirsutum.fasta (fasta header after modifications, step 3)
Lycopersicon_pennellii.fasta.orig (fasta header before modifications, step 3)
Lycopersicon_pennellii.fasta (fasta header after modifications, step 3)

Lycopersicon_hirsutum_vs_Lycopersicon_esculentum.blastn (step 4 and 5)
Lycopersicon_pennellii_vs_Lycopersicon_esculentum.blastn (step 4 and 5)
Lycopersicon_hirsutum_vs_Lycopersicon_esculentum.blastn.all_hits (step 5)
Lycopersicon_pennellii_vs_Lycopersicon_esculentum.blastn.all_hits (step 5)
Lycopersicon_hirsutum_vs_Lycopersicon_esculentum.blastn.id_list (step 5)
Lycopersicon_pennellii_vs_Lycopersicon_esculentum.blastn.id_list (step 5)

Lycopersicon_esculentum.with_hits.IDs_temp (step 5)
Lycopersicon_esculentum.with_hits.IDs (step 5 and 6)
Lycopersicon_esculentum.with_hits.fasta.backup (fasta header before modifications, step 6)
Lycopersicon_esculentum.with_hits.fasta (fasta header before modifications, step 6)
tomato_ABC.fasta (ESTs for CAP3 assembly, step 7 and 8)
tomato_ABC.cap3.out (CAP3 output, step 8, 9 and 10)

tomato_ABC.cap3.out.Info (step 9 and 12)
tomato_alignments (archived directory with "Alignment Files", step 10)
L_ABC_Contigs_All.aln (single file with ALL alignments, step 11)
L_ABC_Contigs_All.aln.MM (output of Python_CAP3_MM_Finder, step 11 and 12)

A_vs_BC_deletions.good A_vs_BC_insertions.good A_vs_BC_substitutions.good (steps 12 - 16)
B_vs_AC_deletions.good B_vs_AC_insertions.good B_vs_AC_substitutions.good (steps 12 - 16)
C_vs_AB_deletions.good C_vs_AB_insertions.good C_vs_AB_substitutions.good (steps 12 - 16)

A_vs_BC_deletions.good.sorted (step 17)
A_vs_BC_insertions.good.sorted (step 17)
A_vs_BC_substitutions.good.sorted (step 17)