/Evannus

Perl scripts used in Euplotes vannus genomic data analysis

GNU General Public License v3.0GPL-3.0

Euplotes vannus genomic analysis

Perl scripts used in Euplotes vannus genomic data analysis

1. Coverage distribution of scaffolds

01scf_coverage_distribution.pl

Usage:

perl 01scf_coverage_distribution.pl  Str.sul_scaffolds_nobac_nomito_noredundancy.fasta

2. Filter out low coverage scaffolds

02scf_coverage_selection.pl

Usage:

perl 02scf_coverage_selection.pl  <genome file>  <coverage_cutoff>  <scaffold_length_cutoff>

3. Separate scaffold into different groups based on telomeres' presence

03scf_telomere_selection.pl

Usage:

perl 03scf_telomere_selection.pl  <genome file>  <output_dir>

4. Split fragments in SAM file into mapped and unmapped after mapping

04split_sam_into_mapped_unmapped.pl

Usage:

perl 04split_sam_into_mapped_unmapped.pl  <SAM file>

5. List names of mapped contigs/scaffolds in SAM file

05list_sam_mapped_targets.pl

Usage:

perl 05list_sam_mapped_targets.pl  <SAM file>

6. Filter out genes without RNA-seq reads mapping

06validation_gene_prediction_byRNAseq.pl

Usage:

perl 06validation_gene_prediction_byRNAseq.pl  <Gene data file>  <RNA-seq mapping list>  <Output file>

7. Detect frameshifting events from output file of BLASTX

07frameshifting_detect_BLASTX_tab.pl

Usage:

perl 07frameshifting_detect_BLASTX_tab.pl  <input_file BLASTX tab>  <output file1 frameshifting BLASTX tab>  <output file2 frameshifting adjacent region>  <frame_distance>

8. Analyze stop codon usage from output file of BLASTX and transcriptome assembly

08stop_codon_usage_BLASTX_tab.pl

Usage:

perl 08stop_codon_usage_BLASTX_tab.pl  <input_file1_transcript_FASTA>  <input_file2_BLASTX_tab>  <output_file1_stop_codon_usage>

9. Detect nanochromosomes containing multiple genes from genome annotation file

09detect_joint_nanochromosome_gff3.pl

Usage:

perl 09detect_joint_nanochromosome_gff3.pl  <input_file>  <output_file1>  <output_file2>  <gap>