Convert MaGeCK RRA sgRNA results to bw tracks

usage: Mageck2bw.py [-h] [-o OUTPUT] -f MAGECK_RRA -b GRNA_BED
                    (--cas9 | --ABE | --CBE) [-g GENOME] [-s CHROM_SIZE]

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        output file name, output_FDR.bw, output_LFC.bw,
                        output_FDR.bdg, output_LFC.bdg (default: output)
  -f MAGECK_RRA, --mageck_RRA MAGECK_RRA
                        mageck_RRA sgRNA summary file (default: None)
  -b GRNA_BED, --gRNA_bed GRNA_BED
                        gRNA bed file, need strand info (default: None)
  --cas9                use cas9 cut site (-3) as gRNA score (default: False)
  --ABE                 ABE mode (default: False)
  --CBE                 CBE mode (default: False)

Genome Info:
  -g GENOME, --genome GENOME
                        genome version: hg19, hg38, mm9, mm10. By default,
                        specifying a genome version will automatically update
                        index file, black list, chrom size and
                        effectiveGenomeSize, unless a user explicitly sets
                        those options. (default: hg19)
  -s CHROM_SIZE, --chrom_size CHROM_SIZE
                        chrome size (default: /home/yli11/Data/Human/hg19/anno
                        tations/hg19.chrom.sizes)

Summary

Generate LFC and FDR tracks given Mageck RRA results.

Input

  1. Mageck RRA sgRNA results

File: /home/yli11/test/ABE_high_vs_low_mageck_RRA_results.sgrna_summary.txt

sgrna   Gene    control_count   treatment_count control_mean    treat_mean      LFC     control_var     adj_var score   p.low   p.high  p.twosided      FDR     high_in_treatment
chr19:13190675-TGCTGCCTGTGTAGAGGGCC     chr19:13190380-13190550 2.3734/6.9212   272.09/293.85   4.6473  282.97  5.652   10.342  11.686  81.417  1       0       0       0       True
chr11:5306112-TACTCATGGTCTATCTCTCC      chr11:5305920-5306090   252.76/250.89   2342.7/2282.8   251.83  2312.8  3.194   1.7444  1243.7  58.439  1       0       0       0       True
chr2:57948343-ACGAGGCCAGGAAGACACAG      chr2:57948080-57948230  386.86/415.27   2447.9/2378.2   401.07  2413    2.586   403.76  2167    43.221  1       0       0       0       True
chr11:5173389-TATCTGAATGACAAGCTGGT      chr11:5173040-5173250   59.334/50.179   623.5/674.32    54.756  648.91  3.543   41.907  204.44  41.554  1       0       0       0       True
chr11:5248516-AGGGCTGGGCATAAAAGTCA      chr11:5248300-5248490   192.24/174.76   1285.7/1348.1   183.5   1316.9  2.8366  152.79  853.54  38.795  1       0       0       0       True
chr11:5264509-GCACTGTAACAAGCTGCACG      chr11:5264320-5264470   315.66/176.49   1586.4/1585.5   246.07  1585.9  2.6832  9683.4  1210    38.519  1       0       0       0       True
chr11:5646581-TATCAGTGTGCACTCAAAGC      chr11:5646340-5646490   354.82/304.53   1641.8/1828.3   329.68  1735.1  2.3923  1264.2  1714.7  33.939  1       8.893e-253      1.7786e-252     1.5791e-249     True
chr11:5256103-TGCGGTGGGGAGATATGTAG      chr11:5255800-5255990   325.15/389.32   1837.3/1794.9   357.23  1816.1  2.3427  2058.9  1887.2  33.582  1       1.5248e-247     3.0495e-247     2.3691e-244     True
chr19:12952224-GCGGGGCCTATAAGAAGGCG     chr19:12952024-12952190 176.82/257.82   1332.8/1270.8   217.32  1301.8  2.5771  3280.6  1043.6  33.57   1       2.3175e-247     4.635e-247      3.2007e-244     True

The sgrna column should contain sgRNA sequence, which could be just sgRNA sequence or any name ending with sgRNA sequence.

  1. gRNA bed file

File: /home/yli11/Data/gRNA_libary/ruopeng_library/gRNA.loci307.bed.sorted

chr11   4167374 4167394 ACAAGCAACAGTTGACCAAC    0       +
chr11   4167375 4167395 CAAGCAACAGTTGACCAACA    0       +
chr11   4167392 4167412 CTCAACAGCAGGTTCCCTGT    0       -
chr11   4167403 4167423 CAGATTACGGGCTCAACAGC    0       -
chr11   4167406 4167426 GTTGAGCCCGTAATCTGCTG    0       +
chr11   4167415 4167435 AAATTTCCTCAGCAGATTAC    0       -
chr11   4167416 4167436 CAAATTTCCTCAGCAGATTA    0       -
chr11   4167441 4167461 AGCAGGCAGTACTCAGGGAC    0       -
chr11   4167446 4167466 AGATAAGCAGGCAGTACTCA    0       -
chr11   4167447 4167467 GAGATAAGCAGGCAGTACTC    0       -

The columns should be chr, start, end, gRNA_sequence, value (not used), strand (required).

Usage

hpcf_interative.sh

module load python/2.7.13

module load ucsc/041619

Mageck2bw.py -f /home/yli11/test/ABE_high_vs_low_mageck_RRA_results.sgrna_summary.txt -b /home/yli11/Data/gRNA_libary/ruopeng_library/gRNA.loci307.bed.sorted --cas9 -o HbF

Output

-rwxrwx--- 1 yli11 chenggrp  254K Mar 10 16:48 HbF.FDR.bdg
-rwxrwx--- 1 yli11 chenggrp  205K Mar 10 16:48 HbF.LFC.bdg
-rwxrwx--- 1 yli11 chenggrp  152K Mar 10 16:48 HbF.FDR.bw
-rwxrwx--- 1 yli11 chenggrp  158K Mar 10 16:48 HbF.LFC.bw

Comments

code @ github.