FLEXIS/Notes.txt at main · NCI-RBL/FLEXIS · GitHub

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# Notes


module load bedops
gtf2bed < gencode.vM23.annotation.gtf > gencode.vM23.annotation.bed


awk '{
    diff = $2 - $3;
    sum += diff;
    sumsq += diff * diff;
    count++;
} END {
    mean = sum / count;
    variance = (sumsq / count) - (mean * mean);
    stdev = (variance > 0 ? sqrt(variance) : 0);
    printf "Mean: %.2f\nStandard Deviation: %.2f\n", mean, stdev;
}' dedNA_EV1_forward_L-tron.bed


Rscript scripts/DiffExp.r results/merged_peaks.5UTR.counts.bed results/merged_peaks.5UTR.DiffExp.tsv
python scripts/DiffExpToBed.py results/merged_peaks.5UTR.DiffExp.tsv results/merged_peaks.5UTR.DiffExp


cat rmsk.mm10.bed sncRNA_nuc.bed | bedtools sort -i - > blacklist.bed

grep '+' mm10.NCBI_RefSeq.UCSC.5UTR.bed | grep -v 'X' > mm10.NCBI_RefSeq.UCSC.5UTR.plus.bed
grep '-' mm10.NCBI_RefSeq.UCSC.5UTR.bed | grep -v 'X' > mm10.NCBI_RefSeq.UCSC.5UTR.minus.bed