CLIP ANALYSIS

makes some useful clip analysis figures for QC and other things.

Requirements:

• HOMER
• EMBOSS
• bedtools
• python 2.7
• matplotlib
• seaborn
• numpy
• pandas
• pybedtools

(or run the run_environments.sh script - don't forget to source activate clip_analysis)

GATK -> eCLIP 0.1.x

• made with table markdown generator (https://www.tablesgenerator.com/markdown_tables#)

	GATK	eCLIP 0.1.7
Demuxed + adapter trimmed reads	204.01_RBFOX2.A01.r*.fqTrTr.fqgz	RBFOX2-204-CLIP_S1_R*.A01_204_01_RBFOX2.adapterTrim.round2.fastq.gz
Repetitive element filtered reads	204.01_RBFOX2.A01.r-.fqTrTrU*.fq	RBFOX2-204-CLIP_S1_R1.A01_204_01_RBFOX2.adapterTrim.round2.rep.bamUnmapped.out.mate*
Unique genome aligned reads	204.01_RBFOX2.A01.r-.fqTrTrU-SoMaSo.bam	RBFOX2-204-CLIP_S1_R1.A01_204_01_RBFOX2.adapterTrim.round2.rmRep.bam
PCR duplicate removed aligned reads	204.01_RBFOX2.A01.r-.fqTrTrU-SoMaSoCpSo.bam	RBFOX2-204-CLIP_S1_R1.A01_204_01_RBFOX2.adapterTrim.round2.rmRep.rmDup.sorted.bam
Barcode merged alignments	204.01_RBFOX2.---.r-.fqTrTrU-SoMaSoCpSoMeV2.bam	204_01_RBFOX2.merged.r2.bam
CLIPper peaks	204.01_RBFOX2.---.r-.fqTrTrU-SoMaSoCpSoMeV2Cl.bed	204_01_RBFOX2.merged.r2.peaks.bed
Input-normalized peaks	204.01_RBFOX2.---.r-.fqTrTrU-SoMaSoCoSoMeV2ClNpCo.bed	204_01.basedon_204_01.peaks.l2inputnormnew.bed.compressed.bed

Usage:

clip_analysis \
--l2fcwithpval_enr_r1 inputs/204_01_RBFOX2.l2fc_significant_regioncalls.txt \  # output from region_based_enrichment (l2fcWithPvalEnr)
--l2fcwithpval_enr_r2 inputs/204_02_RBFOX2.l2fc_significant_regioncalls.txt \
--inp_reads_by_loc_r1 inputs/204_01_RBFOX2.input.broadfeaturecounts.txt \  # output from region_based_enrichment (inputBroadFeatures)
--inp_reads_by_loc_r2 inputs/204_02_RBFOX2.input.broadfeaturecounts.txt \
--pickle_r1 inputs/204_01_RBFOX2.pickle \  # output from clip_analysis_legacy (--pickle FILE.pickle)
--pickle_r2 inputs/204_02_RBFOX2.pickle \
--annotated_files \
inputs/204_01_RBFOX2 \  # output from annotator (*.annotated)
inputs/204_02_RBFOX2 \
--rep_element_parsed_r1_ip inputs/204_01_RBFOX2.combined_w_uniquemap.rmDup.sam.parsed \  # output from rep_element_pipeline (parsed file)
--rep_element_parsed_r1_input inputs/204_INPUT_RBFOX2.combined_w_uniquemap.rmDup.sam.parsed \
--rep_element_parsed_r2_ip inputs/204_02_RBFOX2.combined_w_uniquemap.rmDup.sam.parsed \
--rep_element_parsed_r2_input inputs/204_INPUT_RBFOX2.combined_w_uniquemap.rmDup.sam.parsed \
--regions CDS intron 3utr \  # specify regions of interest (default: CDS intron 3utr 5utr)
--out_file outputs/all_figures.png  # output image file

(or see examples/run_clip_analysis.sh script)