[GET-dev] GFF3 to Wig ?
Erik Garrison
erik.garrison at gmail.com
Fri Jan 7 08:22:40 EST 2011
On Thu, Jan 6, 2011 at 5:31 PM, Alexander Wait Zaranek <
awaitz at post.harvard.edu> wrote:
> 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.)
>
We've been working on format extensions to BAM which will make it applicable
to multiple splits per read fragment.
We didn't consider CGI data, which I believe is a bit different in structure
than the patterns we anticipated. We could add support for it to the
extension.
The latest version of the CGI pipeline, with sample files, is described
> here:
> * http://www.completegenomics.com/sequence-data/download-data/
Does CGI only provide evidence for called alleles, or is this merely done to
make the example data smaller?
> 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
>
> _______________________________________________
> GET-dev mailing list
> GET-dev at lists.freelogy.org
> http://lists.freelogy.org/mailman/listinfo/get-dev
>
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