Hi Luvina, I finally figured out the problem with creating a bigbed file. I have a bed file with the first 12 fields and I wasn't specifying type or an .as file. Now I've been able to create a bigBED a couple different ways with no errors, but with the same problem each time when I go to use them as tracks. I can get it to create one when I use the .as or just by specifying the type.
For example just in case the .as was not quite right I've started just using the following command line to create the bigBed file. ./bedToBigBed -type=bed12 transcripts.allSamples.5s.bed rn4.chrom.sizes transcripts.allSamples.5.bb This seems to work, but the result has one exon. When I convert the bigBed to bed again, I only have the first blockSize and blockStart value the rest of the list has been removed. This is true of the values for the itemRgb column as well. Only the first value in the comma separated list seems to be in the bigBED file(or its not being output back to the .bed file). Here are the first few lines of the bed file(Created from a gtf file output by Cufflinks)(I used a slightly modified python script from Wei Li to create the bed file): chr1 394971 435563 CUFF.1.1 0 + 394971 435563 255,0,0 2 662,325 0,40267 chr1 612645 613322 CUFF.2.1 0 . 612645 613322 255,0,0 1 677 0 chr1 1307207 1307637 CUFF.3.1 2 . 1307207 1307637 255,0,0 1 430 0 chr1 1421742 1422480 CUFF.4.1 0 . 1421742 1422480 255,0,0 1 738 0 chr1 1554721 1557379 CUFF.5.1 3 . 1554721 1557379 255,0,0 1 2658 0 chr1 1615720 1617210 CUFF.6.1 0 . 1615720 1617210 255,0,0 1 1490 0 chr1 1727887 1728699 CUFF.7.1 0 . 1727887 1728699 255,0,0 1 812 0 chr1 1922775 1925965 CUFF.8.1 0 . 1922775 1925965 255,0,0 1 3190 0 chr1 1960722 1961475 CUFF.9.1 0 - 1960722 1961475 255,0,0 2 248,244 0,509 I then sorted using bedSort and ran bedToBigBed. It just seems like in the bigbed file the comma separated lists have been truncated to the first value. Here is the bed file output from converting the bigbed back to bed. chr1 394971 435563 CUFF.1.1 0 + 394971 435563 255 2 662 0 chr1 612645 613322 CUFF.2.1 0 . 612645 613322 255 1 677 0 chr1 1307207 1307637 CUFF.3.1 2 . 1307207 1307637 255 1 430 0 chr1 1421742 1422480 CUFF.4.1 0 . 1421742 1422480 255 1 738 0 chr1 1554721 1557379 CUFF.5.1 3 . 1554721 1557379 255 1 2658 0 chr1 1615720 1617210 CUFF.6.1 0 . 1615720 1617210 255 1 1490 0 chr1 1727887 1728699 CUFF.7.1 0 . 1727887 1728699 255 1 812 0 chr1 1922775 1925965 CUFF.8.1 0 . 1922775 1925965 255 1 3190 0 chr1 1960722 1961475 CUFF.9.1 0 - 1960722 1961475 255 2 248 0 I tried to also create the bigBED using type and an .as file. This would work but only with the following .as file: table RNAIsoRatBrain "RNA Isoforms from BNLX/SHRH RNA Seq" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Transcription start position" uint chromEnd; "Transcription end position" string name; "Name of gene" uint score; "Score" char[1] strand; "+ or - for strand" uint thickStart; "Coding region start" uint thickEnd; "Coding region end" uint reserved; "Used as itemRgb as of 2004-11-22" int blockCount; "Number of blocks" int[blockCount] blockSizes; "Comma separated list of block sizes" int[blockCount] chromStarts; "Start positions relative to chromStart" ) I could not change reserved to itemRgb and it seems like that should be a uint[3] but nothing worked. The last column I thought was supposed to be blockStarts but I just got an error saying it differed from the name expected chromStarts. So I assume the .as file is not correct but it wouldn't run other than with this file. I'd either get an error about the names or the type not matching when I tried to change anything to what I thought it should be. But the resulting bigBED file also seemed to truncate the lists for the itemRgb and for the blockSizes and blockStarts columns. The image looked the same with the file generated with the .as file. I downloaded bedToBigBed again from the website for mac OSX i386. I'm using OS X 10.6.8. I noticed the linux version has been update more recently so I thought I would try it on linux. Do you have any suggestions about what might cause bedToBigBed to truncate the lists after the first element? Thanks, Spencer Spencer Mahaffey Senior Professional Research Assistant University of Colorado Denver School of Medicine [email protected]<mailto:[email protected]> http://phenogen.ucdenver.edu<http://phenogen.ucdenver.edu/> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
