awk -f test-aligned-reads.awk 2hrep1.mapped > 2hrep1.mapped-unk samtools view 0hrep1-15mMm.bam | cut -f 1 > 0hrep1-15mMm.bam.ids0 samtools view 0hrep1-15mMm2.bam | cut -f 1 > 0hrep1-15mMm.bam.ids awk -v fn=0hrep1-15mMm.bam.ids -f test-aligned-reads.awk 0hrep1-15mMm.bam.ids0 > diff reczko@fix:/data/images/proton/DKlab/mr/parclip/paralyzer/PARalyzer_v1_1c$ diff /data/images/proton/DKlab/mr/parclip/shrimp/IL4-15mMm.bam.md.bam.bt /data/images/proton/DKlab/mr/parclip/shrimp/IL4-15mMm2.bam.md.bt | head 1,307c1,594 < 544_3355_2093_F3 - ENSMUST00000070533 1 CGGCGGCGGGCGAGCGGGCGCTG IIIIIIIIIIIIIIIIIIIIIII 0 < 525_1979_22_F3 - ENSMUST00000070533 11 CGAGCGGGCGCTGGAG IIIIIIIIIIIIIIII 0 < 916_2299_924_F3 + ENSMUST00000070533 13 AGCGGGCGCTGGAGTAGGAGC IIIIIIIIIIIIIIIIIIIII 0 < 546_1529_4817_F3 - ENSMUST00000070533 13 AGCGGGCGCTGGAGTAGGAG IIIIIIIIIIIIIIIIIIII 0 < 537_2853_2589_F3 + ENSMUST00000070533 26 GTAGGAGCTGGGGAGCGGCG IIIIIIIIIIIIIIIIIIII 0 < 516_2671_1744_F3 - ENSMUST00000070533 27 TAGGAGCTGGGGAGCGGCGCGG IIIIIIIIIIIIIIIIIIIIII 0 < 538_2116_3189_F3 + ENSMUST00000070533 32 GCTGGGGAGCGGCGCGGC IIIIIIIIIIIIIIIIII 0 < 398_892_5080_F3 + ENSMUST00000070533 37 GGAGCGGCGCGGCCGGGG IIIIIIIIIIIIIIIIII 0 < 581_1650_141_F3 - ENSMUST00000070533 40 GCGGCGCGGCCGGGGAAGGAA IIIIIIIIIIIIIIIIIIIII 0 reczko@fix:/data/images/proton/DKlab/mr/parclip/raw/IL4$ grep -C 2 537_2853_2589_F3 ugc_604_11_F3.csfasta reczko@fix:/data/images/proton/DKlab/mr/parclip/raw/IL4$ cd .. reczko@fix:/data/images/proton/DKlab/mr/parclip/raw$ grep -l 537_2853_2589_F3 */*.csfasta 0hrep1/ugc_604_1_F3.csfasta ugc_604_1/ugc_604_1_F3.csfasta ]0;/data/images/proton/DKlab/mr/parclip/shrimpreczko@max:/data/images/proton/DKlab/mr/parclip/shrimp$ grep 1_507_4741_F3 IGG-15mMm.bam.sam 1_507_4741_F3 0 ENSMUST00000103031 1060 255 25H20M5H * 0 0 TAACAGCTAATGAGAAAGGG * AS:i:160 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:TAaCAGCTaATGAGAAAGGG MD:Z:20 1_507_4741_F3 0 ENSMUST00000025243 1353 255 5H38M7H * 0 0 TGTGATGCTGATGACTCTGATAGTGATCTTGTCTCGGA * AS:i:192 NM:i:2 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:6 XX:Z:TGtgATGCtGATGACTCTGATAgTGATCTTgTCTCgGA MD:Z:27G4A5 1_507_4741_F3 16 ENSMUST00000040008 3248 255 2H19M29H * 0 0 CCCGGCTTTCTCATTCTAG * AS:i:170 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:1 XX:Z:CTAGAATGAGAAAGcCGGG MD:Z:19 1_507_4741_F3 16 ENSMUST00000060043 6684 255 16H21M13H * 0 0 TCTAGCACATCAGAGTCATCA * AS:i:170 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:TGATGACTCTGATgTGcTAGA MD:Z:21 1_507_4741_F3 16 ENSMUST00000088646 5923 255 16H21M13H * 0 0 TCTAGCACATCAGAGTCATCA * AS:i:170 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:TGATGACTCTGATgTGcTAGA MD:Z:21 1_507_4741_F3 16 ENSMUST00000088644 5125 255 16H21M13H * 0 0 TCTAGCACATCAGAGTCATCA * AS:i:170 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:TGATGACTCTGATgTGcTAGA MD:Z:21 1_507_4741_F3 16 ENSMUST00000161802 517 255 16H21M13H * 0 0 TCTAGCACATCAGAGTCATCA * AS:i:170 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:TGATGACTCTGATgTGcTAGA MD:Z:21 1_507_4741_F3 16 ENSMUST00000098915 1934 255 14H30M6H * 0 0 GCCTCGACACGCTGAGACTGCACATGCTCC * AS:i:192 NM:i:2 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:GGaGCATGTgCAGTCTCAGCGTGTCGAGGC MD:Z:3C5A20 1_507_4741_F3 16 ENSMUST00000074510 1787 255 14H30M6H * 0 0 GCCTCGACACGCTGAGACTGCACATGCTCC * AS:i:192 NM:i:2 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:GGaGCATGTgCAGTCTCAGCGTGTCGAGGC MD:Z:3C5A20 1_507_4741_F3 0 ENSMUST00000107468 81 255 1H23M26H * 0 0 TCCTTGGCTACACAGCAACTTCA * AS:i:170 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:3 XX:Z:TCCTTGGCTACaCAGCAaCTtCA MD:Z:23 ]0;/data/images/proton/DKlab/mr/parclip/shrimpreczko@max:/data/images/proton/DKlab/mr/parclip/shrimp$ grep 1_507_4741_F3 IGG-15mMm2.sam 1_507_4741_F3 0 ENSMUST00000103031 1060 255 25H20M5H * 0 0 TAACAGCTAATGAGAAAGGG * AS:i:160 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:TAaCAGCTaATGAGAAAGGG 1_507_4741_F3 0 ENSMUST00000025243 1353 255 5H38M7H * 0 0 TGTGATGCTGATGACTCTGATAGTGATCTTGTCTCGGA * AS:i:192 NM:i:2 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:6 XX:Z:TGtgATGCtGATGACTCTGATAgTGATCTTgTCTCgGA 1_507_4741_F3 16 ENSMUST00000040008 3248 255 2H19M29H * 0 0 CCCGGCTTTCTCATTCTAG * AS:i:170 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:1 XX:Z:CTAGAATGAGAAAGcCGGG 1_507_4741_F3 16 ENSMUST00000060043 6684 255 16H21M13H * 0 0 TCTAGCACATCAGAGTCATCA * AS:i:170 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:TGATGACTCTGATgTGcTAGA 1_507_4741_F3 16 ENSMUST00000088646 5923 255 16H21M13H * 0 0 TCTAGCACATCAGAGTCATCA * AS:i:170 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:TGATGACTCTGATgTGcTAGA 1_507_4741_F3 16 ENSMUST00000088644 5125 255 16H21M13H * 0 0 TCTAGCACATCAGAGTCATCA * AS:i:170 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:TGATGACTCTGATgTGcTAGA 1_507_4741_F3 16 ENSMUST00000161802 517 255 16H21M13H * 0 0 TCTAGCACATCAGAGTCATCA * AS:i:170 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:TGATGACTCTGATgTGcTAGA 1_507_4741_F3 16 ENSMUST00000098915 1934 255 14H30M6H * 0 0 GCCTCGACACGCTGAGACTGCACATGCTCC * AS:i:192 NM:i:2 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:GGaGCATGTgCAGTCTCAGCGTGTCGAGGC 1_507_4741_F3 16 ENSMUST00000074510 1787 255 14H30M6H * 0 0 GCCTCGACACGCTGAGACTGCACATGCTCC * AS:i:192 NM:i:2 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:2 XX:Z:GGaGCATGTgCAGTCTCAGCGTGTCGAGGC 1_507_4741_F3 0 ENSMUST00000107468 81 255 1H23M26H * 0 0 TCCTTGGCTACACAGCAACTTCA * AS:i:170 NM:i:0 CS:Z:T22202010323131123121222123311123220312220020030003 CM:i:3 XX:Z:TCCTTGGCTACaCAGCAaCTtCA