GSE167466

Crosstalk between CRISPR-Cas9 and the human transcriptome

1. Sequenced reads were reformatted to include randomers in read headers with umi_tools (1.0.0).
2. Args: --random-seed 1 --bc-pattern NNNNNNNNNN
3. Reads were then trimmed with cutadapt (1.14).
4. Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
5. Reads were then trimmed once more with cutadapt (1.14) to remove double-ligation events.
6. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -a InvRNA*.fasta (fasta sequences can be found at: https://github.com/YeoLab/eclip/tree/master/example/inputs/)
7. Trimmed reads were then mapped with STAR (2.4.0i) against a human-specific repeat element database (RepBase 18.05).
8. Args: --runThreadN 16 \ --genomeDir human_repbase \ --readFilesIn path/to/read1 \ --outFileNamePrefix out_prefix \ --outReadsUnmapped Fastx \ --outSAMtype BAM Unsorted \ --outSAMattributes All \ --outSAMunmapped Within \ --outSAMattrRGline ID:foo \ --outFilterType BySJout \ --outFilterMultimapNmax 30 \ --outFilterMultimapScoreRange 1 \ --outFilterScoreMin 10 \ --alignEndsType EndToEnd

Supplementary Files (5)

Dataset Citations (1)

Linked Publications (1)