TranscriptClean-simpleNF

Simplified TranscriptClean implementation into Nextflow.

Mandatory inputs

• SAM file (.sam, input with --sam)
• FASTA file (.fasta or .fa, input with --fasta)

Basic Usage

nextflow run transcriptclean.nf \\ 
--sam path/to/file.sam \\
--fasta path/to/file.fasta \\

Optional inputs and params

• Tabular .tab file with splice junctions outputed from STAR alignment for splice junction correction (set --sj_correction true and input with --splice_junctions)
• GTF for splice junction extraction before splice junction correction (set --sj_correction true and input with --gtf)
• VCF for variant-aware correction (set --variant_aware true and input with --vcf)

Test data

Google Drive: https://drive.google.com/drive/folders/193kznkMpT54hbp7fdJnKQiIKnnvWRFKW?usp=sharing