# union of reads /data/images/proton/DKlab/mr/parclip/README-parclip-reads.txt 0hrep1 11483855 reads 11481472 aln (/ 11481472 11483855.0) 0.9997924912845033 0hrep2 5468587 reads 5466814 aln (/ 5466814 5468587.0) 0.9996757846222434 #min_n_reads 0hrep3 16830315 reads 16826478 aln (/ 16826478 16830315.0) 0.9997720185272825 2hrep1 7314203 reads 7312032 aln (/ 7312032 7314203.0) 0.9997031802371359 2hrep2 7493007 reads 7488861 aln (/ 7488861 7493007.0) 0.9994466840882439 2hrep3 9526713 reads 9524176 aln (/ 9524176 9526713.0) 0.999733696186712 6hrep1 16607034 reads 16599071 aln (/ 16599071 16607034.0) 0.9995205043838653 6hrep2 12437144 reads 12434006 aln (/ 12434006 12437144.0) 0.9997476912706004 6hrep3 6165724 reads 6162679 aln (/ 6162679 6165724.0) 0.9995061407224844 IFN 5690230 reads 5688365 aln (/ 5688365 5690230.0) 0.9996722452343754 IGG 5571672 reads 5569824 aln (/ 5569824 5571672.0) 0.9996683221840769 #2nd min IL4 13338085 reads 13334917 aln (/ 13334917 13338085.0) 0.9997624846445348 #merge all replicates cd /data/images/proton/DKlab/mr/parclip/shrimp/ /data/results/tools/samtools/samtools-1.3/samtools merge -@ 3 /data/images/proton/DKlab/mr/parclip/shrimp/merged/0hrep1-merged.bam 0hrep1-15mMm2.bam.md.bam 0hrep2-15mMm.bam.md.bam.srt.bam 0hrep3-15mMm.bam.md.bam.srt.bam /data/results/tools/samtools/samtools-1.3/samtools merge -@ 3 /data/images/proton/DKlab/mr/parclip/shrimp/merged/2hrep1-merged.bam 2hrep3-15mMm2.bam.md.bam 2hrep2-15mMm2.bam.md.bam 2hrep1-15mMm2.bam.md.bam samtools merge -@ 3 /data/images/proton/DKlab/mr/parclip/shrimp/merged/6hrep1-merged.bam 6hrep1-15mMm.bam.md.bam 6hrep2-15mMm.bam.md.bam 6hrep3-15mMm.bam.md.bam (+ 11483855 5468587 16830315) 33782757 (+ 7314203 7493007 9526713) 24333923 (+ 16607034 12437144 6165724 ) 35209902 cd /data/images/proton/DKlab/mr/parclip/shrimp/merged$ for i in *bam do echo $i # add MD flags for bowtie format /data/results/tools/samtools/samtools-1.3/samtools calmd -b $i /data/results/reference/mmu/mm9/mRNA-stranded/Mus_musculus.NCBIM37.64-toMM9.fa >& /dev/null > foo.bam2 samtools view -h foo.bam2 | awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/sam2bowtie.awk > $i.md.bt mv foo.bam2 $i.md.bam done cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d ./myp.sh /data/images/proton/DKlab/mr/parclip/paralyzer/ini-files-union-of-reads/sh.2hrep1.ini &> 2hrep1-uor.log ./myp.sh /data/images/proton/DKlab/mr/parclip/paralyzer/ini-files-union-of-reads/sh.6hrep1.ini &> 6hrep1-uor.log ./myp.sh /data/images/proton/DKlab/mr/parclip/paralyzer/ini-files-union-of-reads/sh.0hrep1.ini &> 0hrep1-uor.log mergeMyPar-all-uor.sh ln -s ../PARalyzer_v1_1b/sh-clusters-IFN.txt2.csv sh-clusters-IFN.txt2-mRNA.csv ln -s ../PARalyzer_v1_1b/sh-clusters-IGG.txt2.csv sh-clusters-IGG.txt2-mRNA.csv ln -s ../PARalyzer_v1_1b/sh-distributions-IFN.txt2.csv sh-distributions-IFN.txt2-mRNA.csv ln -s ../PARalyzer_v1_1b/sh-distributions-IGG.txt2.csv sh-distributions-IGG.txt2-mRNA.csv ln -s ../PARalyzer_v1_1b/sh-groups-IFN.txt2.csv sh-groups-IFN.txt2-mRNA.csv ln -s ../PARalyzer_v1_1b/sh-groups-IGG.txt2.csv sh-groups-IGG.txt2-mRNA.csv At /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_with_sdev are the clusters with the sdev info added, format: EnsemblID = transcript ID ClusterID = unique ID for the cluster ReadCount = number of reads that overlap the cluster by at least 1 nucleotide ModeLocation = coordinate of the location with the highest signal / (signal + background) value ConversionLocationCount = number of unique location where at least 1 conversion occurred ConversionEventCount = total number of conversions that occurred within the cluster NonConversionEventCount = total number of possible conversion events that did not occur ModeScore = score of the highest signal / (signal + background) value AvgConversionPct = average conversion % of all conversions in the group containing the cluster GroupConversionEventCount = number of all conversions in the group containing the cluster SdevConversionPct = sdev of conversion % of all conversions in the group containing the cluster MaxConversionPct = max. conversion % of all conversions in the group containing the cluster #@ (cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1c ./myp.sh /data/images/proton/DKlab/mr/parclip/paralyzer/ini-files-mRNA/sh.2hrep1.ini &> 2hrep1.log2 ./myp.sh /data/images/proton/DKlab/mr/parclip/paralyzer/ini-files-mRNA/sh.2hrep2.ini &> 2hrep2.mRNA-log2 ./myp.sh /data/images/proton/DKlab/mr/parclip/paralyzer/ini-files-mRNA/sh.2hrep3.ini &> 2hrep3.mRNA-log2 ./mergeMyPar-dist-mRNA.sh sh-distributions-2hrep1.txt2 ./mergeMyPar-dist-mRNA.sh sh-distributions-2hrep2.txt2 ./mergeMyPar-dist-mRNA.sh sh-distributions-2hrep3.txt2 ./mergeMyPar-mRNA.sh sh-groups-2hrep1.txt2 ./mergeMyPar-mRNA.sh sh-groups-2hrep2.txt2 ./mergeMyPar-mRNA.sh sh-groups-2hrep3.txt2 ./myp.sh /data/images/proton/DKlab/mr/parclip/paralyzer/ini-files-mRNA/sh.0hrep1.ini &> 0hrep1.log-mRNA & ./mergeMyPar-mRNA.sh sh-groups-0hrep1.txt2 ./mergeMyPar-dist-mRNA.sh sh-distributions-0hrep1.txt2 ./mergeMyPar-mRNA.sh sh-clusters-0hrep1.txt2 ./myp.sh /data/images/proton/DKlab/mr/parclip/paralyzer/ini-files-mRNA/sh.IL4.ini &> IL4.log-mRNA & ./mergeMyPar-mRNA.sh sh-clusters-IL4.txt2 ./mergeMyPar-dist-mRNA.sh sh-distributions-IL4.txt2 ./mergeMyPar-mRNA.sh sh-groups-IL4.txt2 source myp-all2-mRNA.sh ./mergeMyPar2-mRNA.sh ./mergeMyPar.sh sh-clusters-0hrep2.txt2 ./mergeMyPar.sh sh-clusters-0hrep3.txt2 ./mergeMyPar.sh sh-clusters-2hrep1.txt2 ./mergeMyPar.sh sh-clusters-2hrep2.txt2 ./mergeMyPar.sh sh-clusters-2hrep3.txt2 ./mergeMyPar.sh sh-clusters-6hrep1.txt2 ./mergeMyPar.sh sh-clusters-6hrep2.txt2 ./mergeMyPar.sh sh-clusters-6hrep3.txt2 ./mergeMyPar.sh sh-clusters-IGG.txt2 ./mergeMyPar.sh sh-clusters-IL4.txt2 ./mergeMyPar.sh sh-clusters-IFN.txt2 ./mergeMyPar-dist-mRNA.sh sh-distributions-0hrep1.txt2s mv sh-distributions-0hrep1.txt2s-mRNA.csv sh-distributions-0hrep1.txt2-mRNA.csv ./mergeMyPar-dist-mRNA.sh sh-distributions-2hrep1.txt2 ./mergeMyPar-dist-mRNA.sh sh-distributions-6hrep1.txt2 ./mergeMyPar-dist-mRNA.sh sh-distributions-IGG.txt2 ./mergeMyPar-dist-mRNA.sh sh-distributions-IL4.txt2 ./mergeMyPar-dist-mRNA.sh sh-distributions-IFN.txt2 ./mergeMyPar.sh sh-groups-0hrep1.txt2 ./mergeMyPar.sh sh-groups-0hrep2.txt2 ./mergeMyPar.sh sh-groups-0hrep3.txt2 ./mergeMyPar.sh sh-groups-2hrep1.txt2 ./mergeMyPar.sh sh-groups-2hrep2.txt2 ./mergeMyPar.sh sh-groups-2hrep3.txt2 ./mergeMyPar.sh sh-groups-6hrep1.txt2 ./mergeMyPar.sh sh-groups-6hrep2.txt2 ./mergeMyPar.sh sh-groups-6hrep3.txt2 ./mergeMyPar.sh sh-groups-IGG.txt2 ./mergeMyPar.sh sh-groups-IL4.txt2 ./mergeMyPar.sh sh-groups-IFN.txt2 ln -s ../PARalyzer_v1_1b/sh-clusters-0hrep2.txt2.csv sh-clusters-0hrep2.txt2-mRNA.csv ln -s ../PARalyzer_v1_1b/sh-clusters-0hrep3.txt2.csv sh-clusters-0hrep3.txt2-mRNA.csv ln -s ../PARalyzer_v1_1b/sh-distributions-0hrep2.txt2.csv sh-distributions-0hrep2.txt2-mRNA.csv ln -s ../PARalyzer_v1_1b/sh-distributions-0hrep3.txt2.csv sh-distributions-0hrep3.txt2-mRNA.csv ) # paralyzer to bed, more than 5 TtoC for i in sh-clusters*uor-txt2.csv do echo $i awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2bed-gt5tc.awk $i > $i.bed.gt5tc done # link files (for i in /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/sh-distributions*.txt2.csv do ln -s $i done ) #Diff to README*5.txt: no max conv cutoff, direct to bed #get avg+max TtoC (note >100% bug in /data/images/proton/DKlab/mr/parclip/paralyzer/README.PARalyzer_v1_1_src.txt, clipped to 100%) for i in sh-distributions*.uor-txt2.csv do cat $i| awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/get-TtoC-conversionPct-noCutoff2.awk|awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa-dist2bed2.awk > $i".avg.csv3.bed" done # intersect maxTtoC_gt_0.25 with clusters #/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1b/res/recommended_settings_gt5tc/ sh-distributions-0hrep1.uor-txt2.csv.avg.csv.bed sh-distributions-2hrep1.uor-txt2.csv.avg.csv.bed sh-distributions-6hrep1.uor-txt2.csv.avg.csv.bed sh-distributions-IFN.uor-txt2.csv.avg.csv.bed sh-distributions-IGG.uor-txt2.csv.avg.csv.bed sh-distributions-IL4.uor-txt2.csv.avg.csv.bed #with sh-clusters-0hrep1.uor-txt2.csv.bed.gt5tc sh-clusters-2hrep1.uor-txt2.csv.bed.gt5tc sh-clusters-6hrep1.uor-txt2.csv.bed.gt5tc sh-clusters-IFN.uor-txt2.csv.bed.gt5tc sh-clusters-IGG.uor-txt2.csv.bed.gt5tc sh-clusters-IL4.uor-txt2.csv.bed.gt5tc # (note: /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk adds # AvgConversionPct_ConversionEventCount_SdevConversionPct MaxConversionPct # ) is bedtools intersect -a sh-clusters-0hrep1.uor-txt2.csv.bed.gt5tc -b sh-distributions-0hrep1.uor-txt2.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk > sh-clusters-0hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-2hrep1.uor-txt2.csv.bed.gt5tc -b sh-distributions-2hrep1.uor-txt2.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-2hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-6hrep1.uor-txt2.csv.bed.gt5tc -b sh-distributions-6hrep1.uor-txt2.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-6hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-IFN.uor-txt2.csv.bed.gt5tc -b sh-distributions-IFN.uor-txt2.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-IFN.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-IGG.uor-txt2.csv.bed.gt5tc -b sh-distributions-IGG.uor-txt2.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-IGG.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2 bedtools intersect -a sh-clusters-IL4.uor-txt2.csv.bed.gt5tc -b sh-distributions-IL4.uor-txt2.csv.avg.csv3.bed -wa -wb -s |awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/add_conversion_pct2.awk> sh-clusters-IL4.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2 # wc *gt0.25TtoC2 # # strand stats for i in sh-clusters-*csv3.bed.gt5tc.gt0.25TtoC2 do echo $i awk -f ../strandStats1.awk $i done # separate plus strand results for i in sh-clusters-*.csv3.bed.gt5tc.gt0.25TtoC2 do wc $i awk -f ../filterPlusStrand.awk $i > $i.plus wc !$ done 2693902 16163412 425249315 sh-clusters-0hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2 1419122 8514732 224404697 sh-clusters-0hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus 2431181 14587086 386130523 sh-clusters-2hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2 1279777 7678662 203417031 sh-clusters-2hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus 2748566 16491396 431675012 sh-clusters-6hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2 1473462 8840772 231874870 sh-clusters-6hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus #remove IGG regions for i in sh-clusters-*uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus do wc $i bedtools intersect -a $i -b sh-clusters-IGG.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus -v -s |sort -k1,1 -k2,2n > $i.noIGG wc !$ done 1419122 8514732 224404697 sh-clusters-0hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus 1325879 7955274 208937223 sh-clusters-0hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG 1279777 7678662 203417031 sh-clusters-2hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus 1188986 7133916 188342086 sh-clusters-2hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG 1473462 8840772 231874870 sh-clusters-6hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus 1376250 8257500 215771437 sh-clusters-6hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG ## To detect enriched high-scoring clusters, get highest modscore that is not uniformly distributed Rscript /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1c/get_modescore_hist_uor.r modscore_cutoff for IFN 0.957 0.1134793327234 modscore_cutoff for IL4 0.96 0.12 modscore_cutoff for 0h_all_reps 0.964 0.063 modscore_cutoff for 2h_all_reps 0.954 0.057 modscore_cutoff for 6h_all_reps 0.963 0.070 #awk -v th=0.955 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IFN.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IFN.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ # 30743 184458 4532268 /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IFN.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt #awk -v th=0.93 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IL4.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IL4.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ # 19874 119244 3096656 /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-IL4.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt awk -v th=0.955 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ # 423257 2539542 68781651 /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-0hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt awk -v th=0.93 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1.awk /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ # 524205 3145230 85397961 /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-2hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt awk -v th=0.947 -f /data/images/proton/DKlab/mr/parclip/paralyzer/filter_modescore1.awk sh-clusters-6hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG > /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1d/sh-clusters-6hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt wc !$ # 478472 2870832 77455256 /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1c/sh-clusters-6hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt # filter protein_coding_genes and add annotation from /data/results/reference/mmu/mm9/mRNA-stranded/Mus_musculus.NCBIM37.64-toMM9.headers for i in *uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt do awk -f /data/images/proton/DKlab/mr/parclip/paralyzer/pa2annotate1_no_replicates.awk $i |sort -k1,1 -k4,4 -k2,2n -k5,5n > $i.anno.csv done wc *uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno* 22759 sh-clusters-0hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.csv 29853 sh-clusters-2hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.csv 22939 sh-clusters-6hrep1.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.csv 30743 sh-clusters-IFN.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.csv 19874 sh-clusters-IL4.uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno.csv cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1c/res/sampled for i in /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1c/*uor-txt2.csv3.bed.gt5tc.gt0.25TtoC2.plus.noIGG.flt.anno* do ln -s $i done cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1c/res/recommended_settings_gt5tc_gt0.25TtoC2/ cd /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1c/res/recommended_settings_with_sdev cp /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1c/*bed3*anno.csv . cp /data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1c/*csv3*anno.csv . Rscript mapTRtoGenome7.r for i in *2.bed do sort -k1,1 -k2,2n $i | awk -f correct-bed.awk > $i.srt /data/results/tools/gbrowser/bedToBigBed $i.srt /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/mm9.chrom.sizes $i.bb echo "bigDataUrl=http://genomics-lab.fleming.gr/fleming/DKlab/mr/parclip/tracks/"$i.bb done track type=bigBed name="IFN clusters" description="IFN paralyzer" bigDataUrl=http://genomics-lab.fleming.gr/fleming/DKlab/mr/parclip/tracks/IFN-mapped.bb