[GET-dev] GFF3 to Wig ?

Alexander Wait Zaranek awaitz at post.harvard.edu
Thu Jan 6 12:31:38 EST 2011


On Tue, Jan 4, 2011 at 7:10 PM, Leon Peshkin <peshkin at gmail.com> wrote:
>   Could someone point me to a tool which would allow
> to create a SAM/BAM file from GFF3 and then export in Wig/BED files.
> I thing BAM->BED is possible in bamtools, but how about
> GFF3->BAM and BAM->Wig ?
>  I am attaching a chunk of my gff3 file - it is alignment of reads
> against scaffolds.
>
since the PGP gets whole genome and other genomic data from multiple
platforms we convert this data into a simpler format we created for
the PGP.   Most of our data was produced by Complete Genomics and is
not in "BAM" format.   BAM doesn't have a way to faithfully represent
CGI reads due to format limitations.  (The CGI->BAM converters are
lossy, AFAIK.)

The latest version of the CGI pipeline, with sample files, is described here:
* http://www.completegenomics.com/sequence-data/download-data/

Visualizing CGI/Illumina/SOLiD data is definitely an important
project.  It would be great if a community member could volunteer to
take it on!   Perhaps we could use this mailing list to work out a
"spec" for what needs to be done?

Thanks,
Sasha

>
> scaffold38913   alignAssembly-sacc454pasa_LV15  cDNA_match      51483   51536   96      +       .       ID=chain_1;Target=GGWHCZS01CVNEB
> 1 52 +
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      181791  182015  100     +       .       ID=chain_2;Target=GGWHCZS01B8DBA
> 8 232 +
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      182349  182461  98      +       .       ID=chain_2;Target=GGWHCZS01B8DBA
> 233 345 +
> scaffold36953   alignAssembly-sacc454pasa_LV15  cDNA_match      12449   12685   97      -       .       ID=chain_3;Target=GGWHCZS01BYL46
> 1 241 +
> scaffold38915   alignAssembly-sacc454pasa_LV15  cDNA_match      143091  143273  100     +       .       ID=chain_4;Target=GGWHCZS01B68J0
> 1 183 +
> scaffold38408   alignAssembly-sacc454pasa_LV15  cDNA_match      17300   17392   96      -       .       ID=chain_5;Target=GGWHCZS01D8PA1
> 1 92 +
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      153548  153684  99      -       .       ID=chain_6;Target=GGWHCZS01BUD6C
> 8 143 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909581  909657  100     +       .       ID=chain_7;Target=GGWHCZS01B8A85
> 1 77 +
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      154234  154314  95      -       .       ID=chain_8;Target=GGWHCZS01EMFO0
> 1 83 +
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      153545  153735  98      -       .       ID=chain_8;Target=GGWHCZS01EMFO0
> 84 275 +
> scaffold36409   alignAssembly-sacc454pasa_LV15  cDNA_match      261048  261102  100     +       .       ID=chain_9;Target=GGWHCZS01EUQ0J
> 1 55 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909591  909657  100     +       .       ID=chain_10;Target=GGWHCZS01DNMTI
> 1 67 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909602  909657  100     +       .       ID=chain_11;Target=GGWHCZS01CRCLW
> 1 56 +
> scaffold38911   alignAssembly-sacc454pasa_LV15  cDNA_match      143736  143833  98      -       .       ID=chain_12;Target=GGWHCZS01D1K2W
> 1 98 +
> scaffold37916   alignAssembly-sacc454pasa_LV15  cDNA_match      81940   81992   100     +       .       ID=chain_13;Target=GGWHCZS01C6JD5
> 1 53 +
> scaffold37916   alignAssembly-sacc454pasa_LV15  cDNA_match      82836   82926   100     +       .       ID=chain_13;Target=GGWHCZS01C6JD5
> 54 144 +
> scaffold38933   alignAssembly-sacc454pasa_LV15  cDNA_match      135829  135927  98      -       .       ID=chain_14;Target=GGWHCZS01CQ9ZX
> 1 99 +
> scaffold38933   alignAssembly-sacc454pasa_LV15  cDNA_match      134108  134179  95      -       .       ID=chain_14;Target=GGWHCZS01CQ9ZX
> 100 171 +
> scaffold36910   alignAssembly-sacc454pasa_LV15  cDNA_match      94607   94679   97      -       .       ID=chain_15;Target=GGWHCZS01CFNTH
> 1 71 +
> scaffold36910   alignAssembly-sacc454pasa_LV15  cDNA_match      92066   92099   100     -       .       ID=chain_15;Target=GGWHCZS01CFNTH
> 72 105 +
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      154234  154314  97      -       .       ID=chain_16;Target=GGWHCZS01DS3UM
> 1 81 +
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      153545  153735  100     -       .       ID=chain_16;Target=GGWHCZS01DS3UM
> 82 272 +
> scaffold36953   alignAssembly-sacc454pasa_LV15  cDNA_match      12449   12683   97      -       .       ID=chain_17;Target=GGWHCZS01CTGNU
> 1 239 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909592  909664  100     +       .       ID=chain_18;Target=GGWHCZS01CBNFR
> 1 73 +
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      154234  154314  98      -       .       ID=chain_19;Target=GGWHCZS01CR372
> 1 81 +
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      153545  153735  100     -       .       ID=chain_19;Target=GGWHCZS01CR372
> 82 272 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909588  909667  97      +       .       ID=chain_20;Target=GGWHCZS01DOL8E
> 1 80 +
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      182394  182451  98      +       .       ID=chain_21;Target=GGWHCZS01E37KQ
> 1 58 +
> scaffold36407   alignAssembly-sacc454pasa_LV15  cDNA_match      418186  418221  100     +       .       ID=chain_22;Target=GGWHCZS01A7VUK
> 1 36 +
> scaffold36407   alignAssembly-sacc454pasa_LV15  cDNA_match      419038  419166  100     +       .       ID=chain_22;Target=GGWHCZS01A7VUK
> 37 165 +
> scaffold36407   alignAssembly-sacc454pasa_LV15  cDNA_match      419794  419868  100     +       .       ID=chain_22;Target=GGWHCZS01A7VUK
> 166 240 +
> scaffold36421   alignAssembly-sacc454pasa_LV15  cDNA_match      118515  118699  99      -       .       ID=chain_23;Target=GGWHCZS01CJEXS
> 1 184 +
> scaffold37410   alignAssembly-sacc454pasa_LV15  cDNA_match      361706  361809  100     -       .       ID=chain_24;Target=GGWHCZS01BB26P
> 1 104 +
> scaffold37410   alignAssembly-sacc454pasa_LV15  cDNA_match      360904  360952  100     -       .       ID=chain_24;Target=GGWHCZS01BB26P
> 105 153 +
> scaffold37910   alignAssembly-sacc454pasa_LV15  cDNA_match      82980   83092   100     +       .       ID=chain_25;Target=GGWHCZS01DHIW0
> 1 113 -
> scaffold37910   alignAssembly-sacc454pasa_LV15  cDNA_match      83537   83584   94      +       .       ID=chain_25;Target=GGWHCZS01DHIW0
> 114 163 -
> scaffold36430   alignAssembly-sacc454pasa_LV15  cDNA_match      5533    5619    97      -       .       ID=chain_26;Target=GGWHCZS01CINS0
> 1 89 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      912517  912653  97      -       .       ID=chain_27;Target=GGWHCZS01CY8FF
> 1 137 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      912168  912225  91      -       .       ID=chain_27;Target=GGWHCZS01CY8FF
> 138 195 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909589  909659  100     +       .       ID=chain_28;Target=GGWHCZS01CVFMM
> 1 71 +
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      154234  154314  100     -       .       ID=chain_29;Target=GGWHCZS01B40FY
> 1 81 +
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      153547  153735  100     -       .       ID=chain_29;Target=GGWHCZS01B40FY
> 82 270 +
> scaffold36919   alignAssembly-sacc454pasa_LV15  cDNA_match      113299  113345  100     +       .       ID=chain_30;Target=GGWHCZS01DBSZR
> 1 47 +
> scaffold36953   alignAssembly-sacc454pasa_LV15  cDNA_match      12449   12685   97      -       .       ID=chain_31;Target=GGWHCZS01AVC8Y
> 1 235 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909677  909715  100     +       .       ID=chain_32;Target=GGWHCZS01DC0OZ
> 1 39 -
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909891  909920  100     +       .       ID=chain_32;Target=GGWHCZS01DC0OZ
> 40 69 -
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      156139  156176  100     -       .       ID=chain_33;Target=GGWHCZS01CZ1CL
> 1 38 -
> scaffold36419   alignAssembly-sacc454pasa_LV15  cDNA_match      154845  154973  96      -       .       ID=chain_33;Target=GGWHCZS01CZ1CL
> 39 165 -
> scaffold37919   alignAssembly-sacc454pasa_LV15  cDNA_match      122261  122312  96      +       .       ID=chain_34;Target=GGWHCZS01EF1CO
> 1 51 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909683  909715  100     +       .       ID=chain_35;Target=GGWHCZS01C6B5W
> 1 33 -
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909891  909915  100     +       .       ID=chain_35;Target=GGWHCZS01C6B5W
> 34 58 -
> scaffold37910   alignAssembly-sacc454pasa_LV15  cDNA_match      266441  266510  98      +       .       ID=chain_36;Target=GGWHCZS01BR14F
> 1 69 +
> scaffold38922   alignAssembly-sacc454pasa_LV15  cDNA_match      137914  137970  100     -       .       ID=chain_37;Target=GGWHCZS01CPA1V
> 1 57 +
> scaffold37917   alignAssembly-sacc454pasa_LV15  cDNA_match      52798   52892   97      -       .       ID=chain_38;Target=GGWHCZS01CMW2K
> 1 93 +
> scaffold36935   alignAssembly-sacc454pasa_LV15  cDNA_match      22274   22398   100     -       .       ID=chain_39;Target=GGWHCZS01C1GEQ
> 1 125 +
> scaffold38911   alignAssembly-sacc454pasa_LV15  cDNA_match      143736  143833  98      -       .       ID=chain_40;Target=GGWHCZS01CAS23
> 1 98 +
> scaffold36433   alignAssembly-sacc454pasa_LV15  cDNA_match      188     343     98      +       .       ID=chain_41;Target=GGWHCZS01D4XLL
> 1 154 +
> scaffold36926   alignAssembly-sacc454pasa_LV15  cDNA_match      91417   91535   100     -       .       ID=chain_42;Target=GGWHCZS01CIJEU
> 1 119 -
> scaffold36926   alignAssembly-sacc454pasa_LV15  cDNA_match      90394   90498   100     -       .       ID=chain_42;Target=GGWHCZS01CIJEU
> 120 224 -
> scaffold38913   alignAssembly-sacc454pasa_LV15  cDNA_match      51431   51614   99      +       .       ID=chain_43;Target=GGWHCZS01DAAC8
> 1 184 +
> scaffold36414   alignAssembly-sacc454pasa_LV15  cDNA_match      498987  499090  98      +       .       ID=chain_44;Target=GGWHCZS01BIZ3D
> 1 103 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909675  909715  100     +       .       ID=chain_45;Target=GGWHCZS01BLTD9
> 2 42 -
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909891  909913  100     +       .       ID=chain_45;Target=GGWHCZS01BLTD9
> 43 65 -
> scaffold38913   alignAssembly-sacc454pasa_LV15  cDNA_match      51490   51614   99      +       .       ID=chain_46;Target=GGWHCZS01DCKJA
> 1 124 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909524  909715  98      +       .       ID=chain_47;Target=GGWHCZS01CSVIX
> 1 192 -
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909891  909920  100     +       .       ID=chain_47;Target=GGWHCZS01CSVIX
> 193 222 -
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909602  909659  100     +       .       ID=chain_48;Target=GGWHCZS01D0PFQ
> 1 58 +
> scaffold38416   alignAssembly-sacc454pasa_LV15  cDNA_match      6762    6810    97      +       .       ID=chain_49;Target=GGWHCZS01D0TX7
> 1 48 +
> scaffold38416   alignAssembly-sacc454pasa_LV15  cDNA_match      9003    9119    96      +       .       ID=chain_49;Target=GGWHCZS01D0TX7
> 49 165 +
> scaffold38907   alignAssembly-sacc454pasa_LV15  cDNA_match      833004  833038  97      +       .       ID=chain_50;Target=GGWHCZS01CTCD7
> 1 34 +
> scaffold38907   alignAssembly-sacc454pasa_LV15  cDNA_match      838060  838125  100     +       .       ID=chain_50;Target=GGWHCZS01CTCD7
> 35 100 +
> scaffold38907   alignAssembly-sacc454pasa_LV15  cDNA_match      838570  838591  90      +       .       ID=chain_50;Target=GGWHCZS01CTCD7
> 101 122 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909608  909720  98      +       .       ID=chain_51;Target=GGWHCZS01B9U4E
> 1 113 +
> scaffold37912   alignAssembly-sacc454pasa_LV15  cDNA_match      387939  388102  98      +       .       ID=chain_52;Target=GGWHCZS01CC4MR
> 1 163 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909587  909659  100     +       .       ID=chain_53;Target=GGWHCZS01BPMT8
> 1 73 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      908939  909006  98      +       .       ID=chain_54;Target=GGWHCZS01DPL5E
> 1 68 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909592  909715  98      +       .       ID=chain_55;Target=GGWHCZS01BHI27
> 1 124 -
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909891  909920  100     +       .       ID=chain_55;Target=GGWHCZS01BHI27
> 125 154 -
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      908626  908682  96      +       .       ID=chain_56;Target=GGWHCZS01ED8IJ
> 1 57 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909603  909659  100     +       .       ID=chain_57;Target=GGWHCZS01BCQYE
> 1 57 +
> scaffold36907   alignAssembly-sacc454pasa_LV15  cDNA_match      249216  249286  97      +       .       ID=chain_58;Target=GGWHCZS01ATA7N
> 1 69 +
> scaffold36414   alignAssembly-sacc454pasa_LV15  cDNA_match      259865  259962  100     -       .       ID=chain_59;Target=GGWHCZS01DYGRT
> 1 98 +
> scaffold38915   alignAssembly-sacc454pasa_LV15  cDNA_match      116917  117033  97      -       .       ID=chain_60;Target=GGWHCZS01BMW8R
> 1 119 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      911227  911253  100     -       .       ID=chain_61;Target=GGWHCZS01CB12C
> 1 27 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      910741  910883  97      -       .       ID=chain_61;Target=GGWHCZS01CB12C
> 28 170 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      910330  910350  100     -       .       ID=chain_61;Target=GGWHCZS01CB12C
> 171 191 +
> scaffold36935   alignAssembly-sacc454pasa_LV15  cDNA_match      40763   40908   100     -       .       ID=chain_62;Target=GGWHCZS01B2SBA
> 1 146 +
> scaffold36935   alignAssembly-sacc454pasa_LV15  cDNA_match      40763   40920   100     -       .       ID=chain_63;Target=GGWHCZS01EHM0P
> 1 158 +
> scaffold37410   alignAssembly-sacc454pasa_LV15  cDNA_match      611218  611305  100     -       .       ID=chain_64;Target=GGWHCZS01BMOMV
> 1 88 +
> scaffold38919   alignAssembly-sacc454pasa_LV15  cDNA_match      102147  102213  100     +       .       ID=chain_65;Target=GGWHCZS01BVMOL
> 1 67 -
> scaffold38919   alignAssembly-sacc454pasa_LV15  cDNA_match      107678  107788  98      +       .       ID=chain_65;Target=GGWHCZS01BVMOL
> 68 178 -
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909610  909715  97      +       .       ID=chain_66;Target=GGWHCZS01C2HAX
> 1 107 -
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909891  909920  100     +       .       ID=chain_66;Target=GGWHCZS01C2HAX
> 108 137 -
> scaffold37408   alignAssembly-sacc454pasa_LV15  cDNA_match      16679   16777   98      +       .       ID=chain_67;Target=GGWHCZS01BTFN0
> 1 98 +
> scaffold38932   alignAssembly-sacc454pasa_LV15  cDNA_match      135072  135188  95      -       .       ID=chain_68;Target=GGWHCZS01CURJ7
> 1 119 +
> scaffold37907   alignAssembly-sacc454pasa_LV15  cDNA_match      909586  909657  100     +       .       ID=chain_69;Target=GGWHCZS01CB9IJ
> 1 72 +
> scaffold38911   alignAssembly-sacc454pasa_LV15  cDNA_match      136895  136999  100     +       .       ID=chain_70;Target=GGWHCZS01DBI1M
> 1 105 +
> scaffold38911   alignAssembly-sacc454pasa_LV15  cDNA_match      138219  138319  100     +       .       ID=chain_70;Target=GGWHCZS01DBI1M
> 106 206 +
> scaffold38933   alignAssembly-sacc454pasa_LV15  cDNA_match      135829  135906  97      -       .       ID=chain_71;Target=GGWHCZS01C0GBU
> 1 77 +
> scaffold38933   alignAssembly-sacc454pasa_LV15  cDNA_match      134108  134179  95      -       .       ID=chain_71;Target=GGWHCZS01C0GBU
> 78 149 +
>
-- 
Alexander (Sasha) Wait Zaranek, PhD
Research Fellow in Genetics
Director Informatics
Personal Genome Project
Harvard Medical School

http://openwetware.org/wiki/User:Alexander_Wait_Zaranek




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