M2 project under the supervision of Pr. Daniel Gautheret
This project aims to eliminate "normal" transcripts in an RNA-Seq of a tumor using a free-reference approach. The protocol takes as input an RNA-Seq from a cancer patient, then applies a succession of three filters. First a quality filter, only the transcripts which have an abundance greater than or equal to 10 are kept. The second filter: only the transcripts that are absent from the reference transcriptome annotation (GENCODE) and from the polymorphism libraries (gnomAD) are kept. Finally the third filter: only the transcripts which deviate significantly from the distribution of the normal RNA-Seq counts are kept.
