reczko@max:/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings2$ awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/bed2paralyzer1.awk sh-clusters-IFN.txt2.csv2.bed.gt5tc.gt0.25TtoC2.plus.noIGG.anno.csv > sh-clusters-IFN.csv

awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/bed2paralyzer1.awk sh-clusters-IL4.txt2.csv2.bed.gt5tc.gt0.25TtoC2.plus.noIGG.anno.csv > sh-clusters-IL4.csv
awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/bed2paralyzer1.awk sh-clusters-0h.gt0.25TtoC2.plus.noIGG.intersection-all.bed2.gt5tc.details.merged.maxAvg.bed.anno.csv > sh-clusters-0h.csv

awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/bed2paralyzer1.awk sh-clusters-2h.gt0.25TtoC2.plus.noIGG.intersection-all.bed2.gt5tc.details.merged.maxAvg.bed.anno.csv > sh-clusters-2h.csv
awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/bed2paralyzer1.awk sh-clusters-6h.gt0.25TtoC2.plus.noIGG.intersection-all.bed2.gt5tc.details.merged.maxAvg.bed.anno.csv > sh-clusters-6h.csv

#  edit settings in RBP_pipeline2/params$ vi HUR.params
cd /data/images/proton/DKlab/mr/parclip/paralyzer/RBP_pipeline2$ 
./preprocess_HUR
cd /data/images/proton/DKlab/mr/parclip/paralyzer/RBP_pipeline2/data/HUR
reczko@max:/data/images/proton/DKlab/mr/parclip/paralyzer/RBP_pipeline2/data/HUR$ ./run_cERMIT_analysis 


#
Giakas annotated per gene
~/Documents/HuR_PARclip_withHeaders/mRNA-1kIntrons/per_gene/0hs/normtoRNAseq/

input in data/HUR.csv, format:
Chromosome,Strand,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ModeScore,ConversionLocationCount,ConversionEventCount,NonConversionEventCount,FilterType,TranscriptLocation,TranscriptID,GeneName
ENSMUST00000114660,+,682,711,G63872.1,ACTGGCCAATGAGCAGAACTGTTTAAGGCT,26,712,1.0127182323221893,3,18,53,NA,3UTR,ENSMUST00000114660,0610007C21Rik