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Discover Mutation Induced Splice Sites
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README.md
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README.md

MiSplice pipeline

#Song Cao, Reyka Jayasinghe, Qingsong Gao, Mike Wendl#

Pipeline for discovering splice-site creating mutations (SCMs) from RNA-Seq

Please cite the following paper if you use MiSplice pipeline:

Systematic Analysis of Splice-Site-Creating Mutations in Cancer

Jayasinghe RG*, Cao S*, Gao Q, Wendl MC, Vo NS, Reynolds SM, Zhao Y, Climente-González H, Chai S, Wang F, Varghese R, Huang M, Liang W, Wyczalkowski MA, Sengupta S, Li Z, Payne SH, Fenyö D, Miner JH, Walter MJ, The Cancer Genome Atlas Research Network, Vincent B, Eyras E, Chen K, Shmulevich I, Chen F, Ding L, Cell Rep 2018 Apr 3;23(1):270-281

Before running change lines 58,75,78 in MiSplice.pl to reflect personal directories. Bed file for step 2 and step 4 can be found from https://drive.google.com/file/d/14vHI3G45c-xBzpgzs_I43orrKbNJyIVi/view?usp=sharing.

Usage: perl MiSplice.pl <run_folder> <step_number>

<run_folder> = full path of the folder holding mutation annotation file (maf) file for all mutations (misplice.input.maf) and file for the sample list (currently named as Samples).

<step_number> run this pipeline step by step (Either run step 1 to step 9 separately) OR run step 11, then steps 7,8,9 separately.

[1] Split mutation annotation file (MAF) into multiple files for processing

[2] Run discovery step of mutation induced splice creating events

[3] Generate control MAF

[4] Calculate number of supporting reads for control samples

[5] Combine the read count for case and control samples

[6] Calculate the splice score (MaxEntScan)

[7] Split novel sites for bam readcounts

[8] Do bam readcounts

[9] Run rc, hla and expression filtering

File format for input MAF (shortened):

 1	GENE	VPS13D

 2	CHR	1

 3	START	12418559

 4	STOP	12418559

 5	STRAND	+

 6	MUTATION TYPE	Missense_Mutation

 7	TYPE	SNP

 8	REFALLELE	C

 9	TUMORALLELE1	T

10	TUMORALLELE2	T

11	TUMOR SAMPLE	TCGA-02-0047-01A-01D-1490-08

12	NORMAL SAMPLE	TCGA-02-0047-10A-01D-1490-08

13	CANCER TYPE gbm

File format for samples as following (table-delimited with sample id and cancer type): TCGA-02-0047 gbm

TCGA-02-0055    gbm

TCGA-02-2483    gbm

TCGA-02-2485    gbm

TCGA-02-2486    gbm
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