Add bed input, bedpe output, and paf output
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AndreaGuarracino
changed the title
bed input and bedpe outputbed input, bedpe output, and paf output
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Added impg -p scerevisiae7.aln.paf -b x.bed -P | column -t
S288C#1#chrXII 1035507 1000 100000 + S288C#1#chrXII 1035507 1000 100000 99000 99000 255 cg:Z:99000=
SK1#1#chrXII 1075542 15000 49816 + S288C#1#chrXII 1035507 1000 100000 34323 34861 255 cg:Z:200=1X15=1X298=1X1=1X44=1X121=1X196=2X338=1X116=1X71=1X103=1X37=2X7=1X28=1X135=1X26=1X148=1X35=1X4=1X2=2X29=1X109=1X68=1X15=1X256=1X147=1X503=1X12=1X65=1X9=1X109=1X8=1X39=1X30=1X48=1X92=1X20=1X41=1X5=1X26=1X276=1X619=1X20=1X89=1X44=1X182=1X129=1X43=1X14=1X20=1X189=1X12=1X14=1X183=1X196=1X70=1X310=1D3=1X1=1X61=1X20=1X15=1X235=2I25=1X6=1D6=1X62=1X144=....
UWOPS034614#1#chrXII 1075542 70000 92908 + S288C#1#chrXII 1035507 1000 100000 22651 23014 255 cg:Z:55=1X82=6I22=1X380=1X105=1X20=1X95=1X173=1X358=1X111=1X71=1X98=1X14=1X293=1X194=1X158=1X35=1X77=1X410=1X50=1X188=1X237=1D69=1X55=1X134=1X1=1X43=1X153=1X8=1X27=1X22=1X8=1X10=1X27=1X10=1X12=1X3=1X57=1X18=1X104=1X5=1X13=1X71=1X99=1D201=1D442=1X50=1X140=1X37=1X96=1X2=1X83=1X32=1X171=1X130=1X26=1X138=1X34=1X107=1X107=1X236=1X350=1X117=1X62=1I60=1D2=1X151....
Y12#1#chrXII 1054145 90000 104447 + S288C#1#chrXII 1035507 1000 100000 14371 14452 255 cg:Z:54=1X14=1X335=1X936=1D432=1X53=1X728=1X771=1X1127=1X4=1X239=1X414=1X134=1X257=1X160=1X84=1X120=1X71=1X21=1X160=1X128=1D719=1X679=1X314=1X165=1X389=1X77=1X49=1X260=1X486=1X160=1X106=1X138=1D28=1X36=1D1=1X245=1X32=1X260=1X1=2X5=2X46=1X11=1X5=1X11=1X2=1X2=1X5=1X5=1X14=1X95=1X14=1X2=1X59=1X170=1X50=1X20=1X41=1X65=1X518=1X8=1X20=1X17=1X5=1X5=1X11=1X321=1....
S288C#1#chrXII 1035507 500000 900000 + S288C#1#chrXII 1035507 500000 900000 400000 400000 255 cg:Z:400000=
YPS128#1#chrXII 1075542 479121 500000 + S288C#1#chrXII 1035507 500000 900000 20787 20890 255 cg:Z:125=1I998=1X392=18I826=1X354=1X182=1X177=1X307=1X5=1X113=1X173=1X598=1D167=1X106=1X72=1X290=1I51=1X91=1X77=1X464=1X17=6D18=1X2=1X375=1X137=1X781=1X153=1X69=1X2=1I190=1X275=1X89=1X350=1D569=1X66=1X49=1X31=1X28=1X72=1X144=1D164=1X61=1D518=1X473=1X38=1X877=1X223=1X351=1X56=1X58=1I96=1D249=1X242=1X56=1X96=1X11=1X55=1X11=1X1=1X525=1X5=1X524=1X372=1X712=1....
Y12#1#chrXII 1054145 483399 564848 + S288C#1#chrXII 1035507 500000 900000 81041 81489 255 cg:Z:95=1X29=1I1391=9I195=1X321=1X5=1X302=1X1317=1X1458=1X473=6D1326=1X73=1X149=1X2=1I57=10I213=1X636=1D77=4I936=1X1899=1X59=3D126=1X223=1X90=1X472=1D683=1X669=1X804=1X712=1X158=1X848=1X485=2D48=1D78=1X210=1X1951=1X416=1X1172=1X291=1X107=1X266=1X2=1X146=1X143=1X1100=1X493=1X15=1X332=1X512=1X146=1X443=1X101=1X44=1X70=1X13=1X41=1X67=1X28=1X5=1X101=1X139=1X....
UWOPS034614#1#chrXII 1075542 471803 854819 + S288C#1#chrXII 1035507 500000 900000 378942 401759 255 cg:Z:115=1I180=1X555=1X28=1X242=1X173=1X218=9I48=1X20=1X286=1X199=1X3=1X32=1X232=1X63=1X620=1X311=1X26=1X5=1X17=1X95=1X173=1X194=2X282=1X98=1X20=1D167=1X106=1X20=1X161=1X180=1I12=1X38=1X109=1X59=1X142=1X131=1X42=1X122=1X4=12D1X24=3D438=1X5=3I177=1X74=1X260=1X191=1X170=1X123=1X33=1X65=1X2=1I47=1X497=1X115=2X81=1X161=2D381=1X182=1X4=1X250=1X59=1D44=1X38=2D....
Y12#1#chrXII 1054145 585000 780000 + S288C#1#chrXII 1035507 500000 900000 187167 201726 255 cg:Z:139=1X161=1X62=1X20=1X14=1X2=1X363=1X1=1X2=1X5=1X6=1X1=2X22=1X245=1X41=1X107=1X17=1X38=1I68=1X44=1X179=1X71=1X42=1X131=1X449=1X722=1X220=1X7=1D187=1X207=1X557=1X145=1X696=1X2246=1X958=1X383=1X206=1X464=1X624=1X29=1X554=1X1043=1X306=1X171=1I1345=1X26=1I117=1X440=1X188=1X49=1X114=1X1=1X6=1X4=1X167=1X230=1X120=1X319=1X399=1X953=1X744=1X1905=1X160=1X225....
YPS128#1#chrXII 1075542 590000 790000 + S288C#1#chrXII 1035507 500000 900000 192892 206401 255 cg:Z:2648=1X751=1X738=1X1412=1X20=1X603=1X29=1X137=1X28=1X387=1X1522=1I1345=1X26=2I239=1X318=1X353=1X1=1X6=1X4=1X134=1X263=1X440=1X592=1X889=1X215=1X34=1X24=1X339=1X998=1X1067=1X453=1X150=1X31=1X108=1X2=1X32=1X16=1X135=1X38=1X121=1X356=1D384=1X268=1X17=1X17=1X77=1X257=1X1706=1D668=1X2593=1X260=1X24=1I197=1X831=1X180=1D79=1X8=1X80=1X2=1X92=1X14=1X68=1X14=....
SK1#1#chrXII 1075542 730000 865468 + S288C#1#chrXII 1035507 500000 900000 129123 141505 255 cg:Z:46=1X353=1X47=1X143=1X77=1X770=4I497=1X1715=1X623=1X77=1X50=1X254=1X90=1X341=1X835=1X1440=1X53=1X289=1X1063=1X99=1X284=1X506=1X435=1X177=1X1127=1X982=1X65=1X149=1X474=1X687=1X244=1I15=1X342=1X406=1X112=1X9=1X850=1X86=1X44=1X41=1X45=1X7=1X6=1X2=1X7=1X104=1X9=1X263=1X164=1X47=1X20=1X245=2X74=1X109=1X17=1X90=1D154=1X593=1X124=1X60=1X11=1X52=1X13=1X10=1....
Y12#1#chrXII 1054145 860000 872245 + S288C#1#chrXII 1035507 500000 900000 12214 12246 255 cg:Z:884=1X905=1X1443=1X448=1X131=1X4034=1X11=1X29=1X71=1X263=1X199=1X55=1X477=1X413=1X282=1X430=1X349=1X34=1X311=1X358=1X203=1X32=1X1=1X7=1X8=1D290=1X117=1X98=1X94=1X45=1X107=1X26=1X59=....
S288C#1#chrXII 1035507 1000000 2000000 + S288C#1#chrXII 1035507 1000000 2000000 1000000 1000000 255 cg:Z:1000000=
UWOPS034614#1#chrXII 1075542 944197 1000000 + S288C#1#chrXII 1035507 1000000 2000000 55097 55827 255 cg:Z:207=10D95=1X29=1X332=1X70=1X344=1X32=1X269=1X54=1X47=1X142=2X50=1X113=1X11=1X57=1X92=1X15=1X36=1X1=1X35=1X87=1X68=2D9=1X112=1X9=1X174=1X95=1X260=1X80=1X40=1X72=1X2=1X14=1X47=1X6=1X181=1X294=1X532=1X59=1D20=1X332=1X96=1X166=1X2=1X146=1X95=1X947=1X10=2I27=1X63=1X132=1X9=1X41=1I10=1X82=1X47=1X152=1X80=1X56=1X91=1X117=1X91=1X14=1X117=1X39=1I21=1X20=1X20....
Y12#1#chrXII 1054145 980000 1029536 + S288C#1#chrXII 1035507 1000000 2000000 49330 49545 255 cg:Z:444=1X88=1X119=1X152=1X134=1X778=2I132=1X676=1X174=1X37=1X688=1X3219=1D537=1X472=1X96=1X5=1X140=1X26=1X78=1X10=1X21=1X25=1X5=1X47=1X157=1X195=1X4=2X25=1X47=1X186=1X22=1X11=2X20=1X93=1X66=1X19=1X112=1X2=1X158=1X68=1X253=1X1350=1X2135=1X183=1X400=1X73=1X34=1X19=1X74=1X227=1X3=1D133=2I773=1X5=1X475=1X72=1X100=1X95=1X140=1X66=1X2=2I177=1X51=1X38=1X39=1X.... |
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cat x.bed S288C#1#chrXII 1000 100000 S288C#1#chrXII 500000 900000 S288C#1#chrXII 1000000 2000000impg -p scerevisiae7.aln.paf -b x.bed | column -t S288C#1#chrXII 1000 100000 S288C#1#chrXII 1000 100000 SK1#1#chrXII 15000 49816 S288C#1#chrXII 1000 100000 UWOPS034614#1#chrXII 70000 92908 S288C#1#chrXII 1000 100000 Y12#1#chrXII 90000 104447 S288C#1#chrXII 1000 100000 S288C#1#chrXII 500000 900000 S288C#1#chrXII 500000 900000 YPS128#1#chrXII 479121 500000 S288C#1#chrXII 500000 900000 Y12#1#chrXII 483399 564848 S288C#1#chrXII 500000 900000 UWOPS034614#1#chrXII 471803 854819 S288C#1#chrXII 500000 900000 Y12#1#chrXII 585000 780000 S288C#1#chrXII 500000 900000 YPS128#1#chrXII 590000 790000 S288C#1#chrXII 500000 900000 SK1#1#chrXII 730000 865468 S288C#1#chrXII 500000 900000 Y12#1#chrXII 860000 872245 S288C#1#chrXII 500000 900000 S288C#1#chrXII 1000000 2000000 S288C#1#chrXII 1000000 2000000 UWOPS034614#1#chrXII 944197 1000000 S288C#1#chrXII 1000000 2000000 Y12#1#chrXII 980000 1029536 S288C#1#chrXII 1000000 2000000