GSE126263

Musashi-1 is a master regulator of aberrant translation in Group 3 medulloblastoma

1. Sequenced reads were removed of inline barcodes and reformatted to include randomers in read headers with eclipdemux (v0.0.1).
2. Args: --length 10
3. Reads were then trimmed with cutadapt (1.9.1).
4. Args: --match-read-wildcards -O 1 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -g g_adapters.fasta -A A_adapters.fasta -a a_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
5. Reads were then trimmed once more with cutadapt (1.9.1) to remove double-ligation events.
6. Args: --match-read-wildcards -O 5 --times 1 -e 0.1 --quality-cutoff 6 -m 18 -A A_adapters.fasta (fasta sequences generated from parsebarcodes.sh within the eclip 0.1.5+ pipeline)
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 path/to/read2 \ --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 (3)

Dataset Citations (1)

Linked Publications (2)