On Thu, Jan 6, 2011 at 5:31 PM, Alexander Wait Zaranek <span dir="ltr"><<a href="mailto:awaitz@post.harvard.edu">awaitz@post.harvard.edu</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="im">On Tue, Jan 4, 2011 at 7:10 PM, Leon Peshkin <<a href="mailto:peshkin@gmail.com">peshkin@gmail.com</a>> wrote:<br>
> Could someone point me to a tool which would allow<br>
> to create a SAM/BAM file from GFF3 and then export in Wig/BED files.<br>
> I thing BAM->BED is possible in bamtools, but how about<br>
> GFF3->BAM and BAM->Wig ?<br>
> I am attaching a chunk of my gff3 file - it is alignment of reads<br>
> against scaffolds.<br>
><br>
</div>since the PGP gets whole genome and other genomic data from multiple<br>
platforms we convert this data into a simpler format we created for<br>
the PGP. Most of our data was produced by Complete Genomics and is<br>
not in "BAM" format. BAM doesn't have a way to faithfully represent<br>
CGI reads due to format limitations. (The CGI->BAM converters are<br>
lossy, AFAIK.)<br></blockquote><div><br></div><div>We've been working on format extensions to BAM which will make it applicable to multiple splits per read fragment.</div><div><br></div><div>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.</div>
<div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
The latest version of the CGI pipeline, with sample files, is described here:<br>
* <a href="http://www.completegenomics.com/sequence-data/download-data/" target="_blank">http://www.completegenomics.com/sequence-data/download-data/</a></blockquote><div><br></div><div>Does CGI only provide evidence for called alleles, or is this merely done to make the example data smaller?</div>
<div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Visualizing CGI/Illumina/SOLiD data is definitely an important<br>
project. It would be great if a community member could volunteer to<br>
take it on! Perhaps we could use this mailing list to work out a<br>
"spec" for what needs to be done?<br>
<br>
Thanks,<br>
Sasha<br>
<div><div></div><div class="h5"><br>
><br>
> scaffold38913 alignAssembly-sacc454pasa_LV15 cDNA_match 51483 51536 96 + . ID=chain_1;Target=GGWHCZS01CVNEB<br>
> 1 52 +<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 181791 182015 100 + . ID=chain_2;Target=GGWHCZS01B8DBA<br>
> 8 232 +<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 182349 182461 98 + . ID=chain_2;Target=GGWHCZS01B8DBA<br>
> 233 345 +<br>
> scaffold36953 alignAssembly-sacc454pasa_LV15 cDNA_match 12449 12685 97 - . ID=chain_3;Target=GGWHCZS01BYL46<br>
> 1 241 +<br>
> scaffold38915 alignAssembly-sacc454pasa_LV15 cDNA_match 143091 143273 100 + . ID=chain_4;Target=GGWHCZS01B68J0<br>
> 1 183 +<br>
> scaffold38408 alignAssembly-sacc454pasa_LV15 cDNA_match 17300 17392 96 - . ID=chain_5;Target=GGWHCZS01D8PA1<br>
> 1 92 +<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 153548 153684 99 - . ID=chain_6;Target=GGWHCZS01BUD6C<br>
> 8 143 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909581 909657 100 + . ID=chain_7;Target=GGWHCZS01B8A85<br>
> 1 77 +<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 154234 154314 95 - . ID=chain_8;Target=GGWHCZS01EMFO0<br>
> 1 83 +<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 153545 153735 98 - . ID=chain_8;Target=GGWHCZS01EMFO0<br>
> 84 275 +<br>
> scaffold36409 alignAssembly-sacc454pasa_LV15 cDNA_match 261048 261102 100 + . ID=chain_9;Target=GGWHCZS01EUQ0J<br>
> 1 55 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909591 909657 100 + . ID=chain_10;Target=GGWHCZS01DNMTI<br>
> 1 67 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909602 909657 100 + . ID=chain_11;Target=GGWHCZS01CRCLW<br>
> 1 56 +<br>
> scaffold38911 alignAssembly-sacc454pasa_LV15 cDNA_match 143736 143833 98 - . ID=chain_12;Target=GGWHCZS01D1K2W<br>
> 1 98 +<br>
> scaffold37916 alignAssembly-sacc454pasa_LV15 cDNA_match 81940 81992 100 + . ID=chain_13;Target=GGWHCZS01C6JD5<br>
> 1 53 +<br>
> scaffold37916 alignAssembly-sacc454pasa_LV15 cDNA_match 82836 82926 100 + . ID=chain_13;Target=GGWHCZS01C6JD5<br>
> 54 144 +<br>
> scaffold38933 alignAssembly-sacc454pasa_LV15 cDNA_match 135829 135927 98 - . ID=chain_14;Target=GGWHCZS01CQ9ZX<br>
> 1 99 +<br>
> scaffold38933 alignAssembly-sacc454pasa_LV15 cDNA_match 134108 134179 95 - . ID=chain_14;Target=GGWHCZS01CQ9ZX<br>
> 100 171 +<br>
> scaffold36910 alignAssembly-sacc454pasa_LV15 cDNA_match 94607 94679 97 - . ID=chain_15;Target=GGWHCZS01CFNTH<br>
> 1 71 +<br>
> scaffold36910 alignAssembly-sacc454pasa_LV15 cDNA_match 92066 92099 100 - . ID=chain_15;Target=GGWHCZS01CFNTH<br>
> 72 105 +<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 154234 154314 97 - . ID=chain_16;Target=GGWHCZS01DS3UM<br>
> 1 81 +<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 153545 153735 100 - . ID=chain_16;Target=GGWHCZS01DS3UM<br>
> 82 272 +<br>
> scaffold36953 alignAssembly-sacc454pasa_LV15 cDNA_match 12449 12683 97 - . ID=chain_17;Target=GGWHCZS01CTGNU<br>
> 1 239 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909592 909664 100 + . ID=chain_18;Target=GGWHCZS01CBNFR<br>
> 1 73 +<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 154234 154314 98 - . ID=chain_19;Target=GGWHCZS01CR372<br>
> 1 81 +<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 153545 153735 100 - . ID=chain_19;Target=GGWHCZS01CR372<br>
> 82 272 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909588 909667 97 + . ID=chain_20;Target=GGWHCZS01DOL8E<br>
> 1 80 +<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 182394 182451 98 + . ID=chain_21;Target=GGWHCZS01E37KQ<br>
> 1 58 +<br>
> scaffold36407 alignAssembly-sacc454pasa_LV15 cDNA_match 418186 418221 100 + . ID=chain_22;Target=GGWHCZS01A7VUK<br>
> 1 36 +<br>
> scaffold36407 alignAssembly-sacc454pasa_LV15 cDNA_match 419038 419166 100 + . ID=chain_22;Target=GGWHCZS01A7VUK<br>
> 37 165 +<br>
> scaffold36407 alignAssembly-sacc454pasa_LV15 cDNA_match 419794 419868 100 + . ID=chain_22;Target=GGWHCZS01A7VUK<br>
> 166 240 +<br>
> scaffold36421 alignAssembly-sacc454pasa_LV15 cDNA_match 118515 118699 99 - . ID=chain_23;Target=GGWHCZS01CJEXS<br>
> 1 184 +<br>
> scaffold37410 alignAssembly-sacc454pasa_LV15 cDNA_match 361706 361809 100 - . ID=chain_24;Target=GGWHCZS01BB26P<br>
> 1 104 +<br>
> scaffold37410 alignAssembly-sacc454pasa_LV15 cDNA_match 360904 360952 100 - . ID=chain_24;Target=GGWHCZS01BB26P<br>
> 105 153 +<br>
> scaffold37910 alignAssembly-sacc454pasa_LV15 cDNA_match 82980 83092 100 + . ID=chain_25;Target=GGWHCZS01DHIW0<br>
> 1 113 -<br>
> scaffold37910 alignAssembly-sacc454pasa_LV15 cDNA_match 83537 83584 94 + . ID=chain_25;Target=GGWHCZS01DHIW0<br>
> 114 163 -<br>
> scaffold36430 alignAssembly-sacc454pasa_LV15 cDNA_match 5533 5619 97 - . ID=chain_26;Target=GGWHCZS01CINS0<br>
> 1 89 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 912517 912653 97 - . ID=chain_27;Target=GGWHCZS01CY8FF<br>
> 1 137 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 912168 912225 91 - . ID=chain_27;Target=GGWHCZS01CY8FF<br>
> 138 195 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909589 909659 100 + . ID=chain_28;Target=GGWHCZS01CVFMM<br>
> 1 71 +<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 154234 154314 100 - . ID=chain_29;Target=GGWHCZS01B40FY<br>
> 1 81 +<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 153547 153735 100 - . ID=chain_29;Target=GGWHCZS01B40FY<br>
> 82 270 +<br>
> scaffold36919 alignAssembly-sacc454pasa_LV15 cDNA_match 113299 113345 100 + . ID=chain_30;Target=GGWHCZS01DBSZR<br>
> 1 47 +<br>
> scaffold36953 alignAssembly-sacc454pasa_LV15 cDNA_match 12449 12685 97 - . ID=chain_31;Target=GGWHCZS01AVC8Y<br>
> 1 235 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909677 909715 100 + . ID=chain_32;Target=GGWHCZS01DC0OZ<br>
> 1 39 -<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909891 909920 100 + . ID=chain_32;Target=GGWHCZS01DC0OZ<br>
> 40 69 -<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 156139 156176 100 - . ID=chain_33;Target=GGWHCZS01CZ1CL<br>
> 1 38 -<br>
> scaffold36419 alignAssembly-sacc454pasa_LV15 cDNA_match 154845 154973 96 - . ID=chain_33;Target=GGWHCZS01CZ1CL<br>
> 39 165 -<br>
> scaffold37919 alignAssembly-sacc454pasa_LV15 cDNA_match 122261 122312 96 + . ID=chain_34;Target=GGWHCZS01EF1CO<br>
> 1 51 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909683 909715 100 + . ID=chain_35;Target=GGWHCZS01C6B5W<br>
> 1 33 -<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909891 909915 100 + . ID=chain_35;Target=GGWHCZS01C6B5W<br>
> 34 58 -<br>
> scaffold37910 alignAssembly-sacc454pasa_LV15 cDNA_match 266441 266510 98 + . ID=chain_36;Target=GGWHCZS01BR14F<br>
> 1 69 +<br>
> scaffold38922 alignAssembly-sacc454pasa_LV15 cDNA_match 137914 137970 100 - . ID=chain_37;Target=GGWHCZS01CPA1V<br>
> 1 57 +<br>
> scaffold37917 alignAssembly-sacc454pasa_LV15 cDNA_match 52798 52892 97 - . ID=chain_38;Target=GGWHCZS01CMW2K<br>
> 1 93 +<br>
> scaffold36935 alignAssembly-sacc454pasa_LV15 cDNA_match 22274 22398 100 - . ID=chain_39;Target=GGWHCZS01C1GEQ<br>
> 1 125 +<br>
> scaffold38911 alignAssembly-sacc454pasa_LV15 cDNA_match 143736 143833 98 - . ID=chain_40;Target=GGWHCZS01CAS23<br>
> 1 98 +<br>
> scaffold36433 alignAssembly-sacc454pasa_LV15 cDNA_match 188 343 98 + . ID=chain_41;Target=GGWHCZS01D4XLL<br>
> 1 154 +<br>
> scaffold36926 alignAssembly-sacc454pasa_LV15 cDNA_match 91417 91535 100 - . ID=chain_42;Target=GGWHCZS01CIJEU<br>
> 1 119 -<br>
> scaffold36926 alignAssembly-sacc454pasa_LV15 cDNA_match 90394 90498 100 - . ID=chain_42;Target=GGWHCZS01CIJEU<br>
> 120 224 -<br>
> scaffold38913 alignAssembly-sacc454pasa_LV15 cDNA_match 51431 51614 99 + . ID=chain_43;Target=GGWHCZS01DAAC8<br>
> 1 184 +<br>
> scaffold36414 alignAssembly-sacc454pasa_LV15 cDNA_match 498987 499090 98 + . ID=chain_44;Target=GGWHCZS01BIZ3D<br>
> 1 103 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909675 909715 100 + . ID=chain_45;Target=GGWHCZS01BLTD9<br>
> 2 42 -<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909891 909913 100 + . ID=chain_45;Target=GGWHCZS01BLTD9<br>
> 43 65 -<br>
> scaffold38913 alignAssembly-sacc454pasa_LV15 cDNA_match 51490 51614 99 + . ID=chain_46;Target=GGWHCZS01DCKJA<br>
> 1 124 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909524 909715 98 + . ID=chain_47;Target=GGWHCZS01CSVIX<br>
> 1 192 -<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909891 909920 100 + . ID=chain_47;Target=GGWHCZS01CSVIX<br>
> 193 222 -<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909602 909659 100 + . ID=chain_48;Target=GGWHCZS01D0PFQ<br>
> 1 58 +<br>
> scaffold38416 alignAssembly-sacc454pasa_LV15 cDNA_match 6762 6810 97 + . ID=chain_49;Target=GGWHCZS01D0TX7<br>
> 1 48 +<br>
> scaffold38416 alignAssembly-sacc454pasa_LV15 cDNA_match 9003 9119 96 + . ID=chain_49;Target=GGWHCZS01D0TX7<br>
> 49 165 +<br>
> scaffold38907 alignAssembly-sacc454pasa_LV15 cDNA_match 833004 833038 97 + . ID=chain_50;Target=GGWHCZS01CTCD7<br>
> 1 34 +<br>
> scaffold38907 alignAssembly-sacc454pasa_LV15 cDNA_match 838060 838125 100 + . ID=chain_50;Target=GGWHCZS01CTCD7<br>
> 35 100 +<br>
> scaffold38907 alignAssembly-sacc454pasa_LV15 cDNA_match 838570 838591 90 + . ID=chain_50;Target=GGWHCZS01CTCD7<br>
> 101 122 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909608 909720 98 + . ID=chain_51;Target=GGWHCZS01B9U4E<br>
> 1 113 +<br>
> scaffold37912 alignAssembly-sacc454pasa_LV15 cDNA_match 387939 388102 98 + . ID=chain_52;Target=GGWHCZS01CC4MR<br>
> 1 163 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909587 909659 100 + . ID=chain_53;Target=GGWHCZS01BPMT8<br>
> 1 73 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 908939 909006 98 + . ID=chain_54;Target=GGWHCZS01DPL5E<br>
> 1 68 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909592 909715 98 + . ID=chain_55;Target=GGWHCZS01BHI27<br>
> 1 124 -<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909891 909920 100 + . ID=chain_55;Target=GGWHCZS01BHI27<br>
> 125 154 -<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 908626 908682 96 + . ID=chain_56;Target=GGWHCZS01ED8IJ<br>
> 1 57 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909603 909659 100 + . ID=chain_57;Target=GGWHCZS01BCQYE<br>
> 1 57 +<br>
> scaffold36907 alignAssembly-sacc454pasa_LV15 cDNA_match 249216 249286 97 + . ID=chain_58;Target=GGWHCZS01ATA7N<br>
> 1 69 +<br>
> scaffold36414 alignAssembly-sacc454pasa_LV15 cDNA_match 259865 259962 100 - . ID=chain_59;Target=GGWHCZS01DYGRT<br>
> 1 98 +<br>
> scaffold38915 alignAssembly-sacc454pasa_LV15 cDNA_match 116917 117033 97 - . ID=chain_60;Target=GGWHCZS01BMW8R<br>
> 1 119 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 911227 911253 100 - . ID=chain_61;Target=GGWHCZS01CB12C<br>
> 1 27 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 910741 910883 97 - . ID=chain_61;Target=GGWHCZS01CB12C<br>
> 28 170 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 910330 910350 100 - . ID=chain_61;Target=GGWHCZS01CB12C<br>
> 171 191 +<br>
> scaffold36935 alignAssembly-sacc454pasa_LV15 cDNA_match 40763 40908 100 - . ID=chain_62;Target=GGWHCZS01B2SBA<br>
> 1 146 +<br>
> scaffold36935 alignAssembly-sacc454pasa_LV15 cDNA_match 40763 40920 100 - . ID=chain_63;Target=GGWHCZS01EHM0P<br>
> 1 158 +<br>
> scaffold37410 alignAssembly-sacc454pasa_LV15 cDNA_match 611218 611305 100 - . ID=chain_64;Target=GGWHCZS01BMOMV<br>
> 1 88 +<br>
> scaffold38919 alignAssembly-sacc454pasa_LV15 cDNA_match 102147 102213 100 + . ID=chain_65;Target=GGWHCZS01BVMOL<br>
> 1 67 -<br>
> scaffold38919 alignAssembly-sacc454pasa_LV15 cDNA_match 107678 107788 98 + . ID=chain_65;Target=GGWHCZS01BVMOL<br>
> 68 178 -<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909610 909715 97 + . ID=chain_66;Target=GGWHCZS01C2HAX<br>
> 1 107 -<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909891 909920 100 + . ID=chain_66;Target=GGWHCZS01C2HAX<br>
> 108 137 -<br>
> scaffold37408 alignAssembly-sacc454pasa_LV15 cDNA_match 16679 16777 98 + . ID=chain_67;Target=GGWHCZS01BTFN0<br>
> 1 98 +<br>
> scaffold38932 alignAssembly-sacc454pasa_LV15 cDNA_match 135072 135188 95 - . ID=chain_68;Target=GGWHCZS01CURJ7<br>
> 1 119 +<br>
> scaffold37907 alignAssembly-sacc454pasa_LV15 cDNA_match 909586 909657 100 + . ID=chain_69;Target=GGWHCZS01CB9IJ<br>
> 1 72 +<br>
> scaffold38911 alignAssembly-sacc454pasa_LV15 cDNA_match 136895 136999 100 + . ID=chain_70;Target=GGWHCZS01DBI1M<br>
> 1 105 +<br>
> scaffold38911 alignAssembly-sacc454pasa_LV15 cDNA_match 138219 138319 100 + . ID=chain_70;Target=GGWHCZS01DBI1M<br>
> 106 206 +<br>
> scaffold38933 alignAssembly-sacc454pasa_LV15 cDNA_match 135829 135906 97 - . ID=chain_71;Target=GGWHCZS01C0GBU<br>
> 1 77 +<br>
> scaffold38933 alignAssembly-sacc454pasa_LV15 cDNA_match 134108 134179 95 - . ID=chain_71;Target=GGWHCZS01C0GBU<br>
> 78 149 +<br>
><br>
</div></div><font color="#888888">--<br>
Alexander (Sasha) Wait Zaranek, PhD<br>
Research Fellow in Genetics<br>
Director Informatics<br>
Personal Genome Project<br>
Harvard Medical School<br>
<br>
<a href="http://openwetware.org/wiki/User:Alexander_Wait_Zaranek" target="_blank">http://openwetware.org/wiki/User:Alexander_Wait_Zaranek</a><br>
</font><div><div></div><div class="h5"><br>
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</div></div></blockquote></div><br>