GSE232599

Systematic identification of RNA-binding proteins and tethered domains that activate exon splicing inclusion

1. Data was processed using Skipper, available at: http://github.com/yeolab/skipper
2. Reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using skewer.
3. Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with fastp
4. Extracted reads were aligned using STAR: --alignEndsType EndToEnd --genomeDir {params.star_sjdb} --genomeLoad NoSharedMemory --outBAMcompression 10 --outFileNamePrefix {params.outprefix} --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outSAMmultNmax 1 --outMultimapperOrder Random --outFilterScoreMin 10 --outFilterType BySJout --limitOutSJcollapsed 5000000 --outReadsUnmapped None --outSAMattrRGline ID:{wildcards.replicate_label} --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped Within --readFilesCommand zcat --outStd Log --readFilesIn {input.fq} --runMode alignReads --runThreadN {threads}
5. Custom scripts called reproducible enriched windows and repetitive elements as part of Skipper

Dataset Citations (1)

Linked Publications (2)