cDNA Generator module

Description of the module: The function of this module is to generate cdDNA based on mRNA transcript seuqences and the coresponding priming probabilities.

Input files

transcript_copies (csv-formatted) containing:

• ID of transcript
• ID of parent transcript
• copy number

Eample

[ID of transcript] [ID of parent transcript] [copy number]

transcript_sequences (fasta-formatted) containing:

• ID of transcript

Eample

> [ID of transcript] AGUGACGUUAGACCAGAUAGAC....

priming_sites (gtf-formatted) containing:

• ID of transcript
• Position of priming site
• Binding likelihood of priming site

Eample

[ID of transcript] ... [Position of priming site]... [Binding likelihood of priming site]

Output files

cDNA (fasta-formatted) containing:

• cDNA sequence ID
• Uniquie cDNA sequence

cDNA_counts (csv-formatted) containing:

• cDNA sequence ID
• cDNA copy number