Scripts used for data analysis are in scripts/ folder:
- Aligned lengths analysis:
aligned_lengths.py - Aligned lengths analysis (Smith-Waterman alignment):
sw_alignment.py - Errors analysis:
compare_error_rate.py - K-mer identity analysis:
kmer_stats.py - TSS/Poly-A sites analysis:
find_tss_polya.py - Intron chains comparison:
compare_introns.py - Alternative splicing analysis:
alt_splicing.py - Analysis of introns w/respect to read quality:
intron_chain_q.pyandintron_splice_quality.py
Scripts located in the root directory:
- Assign reads to isoforms:
assign_reads_to_isoforms.py - Correct spliced alignments:
correct_spliced_alignments.py - Convert GTF to gffutils database:
gtf2db.py