SPARKS: Splicing Profile Analysis Identifying Key RBPs in Alternative Splicing Changes

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S plicing P rofile A nalysis using R BP K D/KO S ignatures ( SPARKS ) identifies the RBPs most responsible for AS changes in th

Code Snippets

shell:
    'curl -L \'{params.url}\''
    ' -o {output.ref_file}'
    ' 1> {log.out}'
    ' 2> {log.err}'

SnakeMake From line 61 of main/Snakefile

shell:
    ' gunzip -c {input.gz}'
    ' 1> {output.un_gz}'
    ' 2> {log.err}'

SnakeMake From line 82 of main/Snakefile

shell:
    ' cd {params.ref_dir}'
    ' && tar -xvf {params.gz}'
    ' {params.idx}'
    ' {params.to_genes}'
    ' 1> {params.log_out}'
    ' 2> {params.log_err}'

SnakeMake From line 108 of main/Snakefile

shell:
    'mkdir -p {output.ref}'
    ' && {params.conda_wrapper} STAR'
    ' --runThreadN {threads}'
    ' --runMode genomeGenerate'
    ' --genomeDir {output.ref}'
    ' --genomeFastaFiles {input.fasta}'
    ' --sjdbGTFfile {input.gtf}'
    ' --sjdbOverhang 99'
    ' 1> {log.out}'
    ' 2> {log.err}'

SnakeMake STAR From line 131 of main/Snakefile

shell:
    'mkdir -p {params.out_prefix}'
    ' && {params.conda_wrapper} STAR'
    ' --genomeDir {input.star_reference}'
    ' --sjdbGTFfile {input.gtf}'
    ' --runThreadN {threads}'
    ' --outSAMunmapped Within'
    ' --twopassMode Basic'
    ' --outSAMtype BAM SortedByCoordinate'
    ' --limitBAMsortRAM 24489245788'
    ' --outFilterType BySJout'
    ' --outFilterMultimapNmax 20'
    ' --alignSJoverhangMin 8'
    ' --alignSJDBoverhangMin 1'
    ' --outFilterMismatchNmax 999'
    ' --outFilterMismatchNoverLmax 0.04'
    ' --alignIntronMin 20'
    ' --alignIntronMax 1000000'
    ' --alignMatesGapMax 1000000'
    ' --seedSearchStartLmax 30'
    ' --alignEndsType EndToEnd'
    ' --readFilesIn {params.read_files_in}'
    ' --outFileNamePrefix {params.out_prefix}/'
    ' {params.read_files_command}'
    ' 1> {log.out}'
    ' 2> {log.err}'
    ' && mv {params.star_bam_path} {output.bam}'
    ' 1>> {log.out}'
    ' 2>> {log.err}'
    ' && {params.conda_wrapper} samtools'
    ' index {output.bam}'
    ' 1>> {log.out}'
    ' 2>> {log.err}'

SnakeMake SAMtools STAR From line 202 of main/Snakefile

shell:
    '{params.conda_wrapper} python'
    ' {params.script}'
    ' --bam {input.bam}'
    ' --dot-rmats {output.dot_rmats}'
    ' --tmp-dir {params.tmp_dir}'
    ' --out-dir {params.out_dir}'
    ' --b1 {params.b1}'
    ' --gtf {input.gtf}'
    ' --read-length {params.read_length}'
    ' {params.is_paired}'
    ' 1> {log.out}'
    ' 2> {log.err}'

SnakeMake From line 266 of main/Snakefile

shell:
    '{params.conda_wrapper} python'
    ' {params.script}'
    ' --tmp-dir {params.tmp_dir}'
    ' --out-dir {params.out_dir}'
    ' --b1 {output.b1}'
    ' --b2 {output.b2}'
    ' --gtf {input.gtf}'
    ' --read-length {params.read_length}'
    ' --num-threads {threads}'
    ' {params.dot_rmats_files}'
    ' {params.b1_bams}'
    ' {params.b2_bams}'
    ' 1> {log.out}'
    ' 2> {log.err}'

SnakeMake From line 379 of main/Snakefile

shell:
    '{params.conda_wrapper} python'
    ' {params.script}'
    ' {params.rmats_out_dir}'
    ' {params.out_dir}'
    ' --na_filter'
    ' --coverage_filter'
    ' --event {wildcards.event_type}'
    ' --tissue {wildcards.cancer_type}'
    ' --event_annotation'
    ' --sample {input.b1}'
    ' {params.two_group}'
    ' 1> {log.out}'
    ' 2> {log.err}'

SnakeMake From line 438 of main/Snakefile

shell:
    '{params.conda_wrapper} python'
    ' {params.script}'
    ' {input.merged}'
    ' {params.out_dir}'
    ' --cancer_type {wildcards.cancer_type}'
    ' --rna'
    ' 1> {log.out}'
    ' 2> {log.err}'

SnakeMake From line 474 of main/Snakefile

shell:
    '{params.conda_wrapper} python'
    ' {params.script}'
    ' {params.rmats_dir}'
    ' {params.matrix_dir}'
    ' {wildcards.cancer_type}'
    ' 1> {log.out}'
    ' 2> {log.err}'

SnakeMake From line 523 of main/Snakefile

shell:
    '{params.conda_wrapper}'
    ' {params.r1_view_command}'
    ' > {output.tmp_r1}'
    ' 2> {log.err}'
    ' && {params.conda_wrapper}'
    ' {params.r2_view_command}'
    ' > {output.tmp_r2}'
    ' 2>> {log.err}'
    ' && {params.conda_wrapper}'
    ' kallisto quant'
    ' -i {input.idx}'
    ' -o {params.out_dir}'
    ' {output.tmp_r1}'
    ' {params.kallisto_r2}'
    ' {params.single_end}'
    ' 1> {log.out}'
    ' 2>> {log.err}'

SnakeMake Quant kallisto From line 591 of main/Snakefile

shell:
    '{params.conda_wrapper} python'
    ' {params.script}'
    ' {params.in_dir}'
    ' {params.out_dir}'
    ' {wildcards.cancer_type}'
    ' --transcripts-to-genes {input.to_genes}'
    ' 1> {log.out}'
    ' 2> {log.err}'

SnakeMake From line 643 of main/Snakefile

shell:
    '{params.conda_wrapper} Rscript'
    ' {params.script}'
    ' --exp {input.exp_matrix}'
    ' --cancer_type {wildcards.cancer_type}'
    ' {params.sparks_lib}'
    ' {params.psi}'
    ' {params.anno}'
    ' {params.mats}'
    ' 1> {log.out}'
    ' 2> {log.err}'