Hello Jingjing, You can read more about the bedGraph format here:
http://genome.ucsc.edu/goldenPath/help/bedgraph.html This format only has 4 fields so it will not be possible to include the 5th column you list below ("experiment1" etc). One of our developers also had this to say about your questions: You will also need separate files for + and - strands to get values plotted in the same place with two different graphs. You can make the values in one negative and positive in the other, and thus the two graphs can appear next to each other and look somewhat like one graph. Note that you want to be using bigWig and not GFF3 format. You can read more about the bigWig format here: http://genome.ucsc.edu/goldenPath/help/bigWig.html You can also read more about the difference between the different formats here: http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format Best regards, Pauline Fujita, UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 07/27/11 16:34, JINGJING JIN wrote: > I think the BedGraph Track Format may be fit for me. > > Because my dataset is also like this: > > chromA + startposition1 end position1 dataValue1 experiment1 > chromA - startposition2 end position2 dataValue2 experiment1 > .... > chromB + startposition2 end position2 dataValue2 experiment1 > chromB - startposition2 end position2 dataValue2 experiment1 > ..... > > chromA + startposition1 end position1 dataValue1 experiment2 > chromA - startposition2 end position2 dataValue2 experiment2 > .... > chromB + startposition2 end position2 dataValue2 experiment2 > chromB - startposition2 end position2 dataValue2 experiment2 > ..... > I also have several experiment for different chromosome. Can I put > them in one file? > In addition, I have different value for the (+/-) strand for the same > chromosome, Can I draw them in one graph, the +strand is on the top > and - strand is on the below? > > In additon, I don't know if I use the BedGraph format file, I should > use which demand to store this file into my mysql database? Like for > example, like for the wig format, in the final gff3 file, we can add > this: > ctgA . microarray_oligo 1 50000 . . . > Name=example;wigfile=/var/www/gbrowse2/databases/volvox > > Do I need to convert the bedgraph file into gff3 file? > > Thanks! > > jingjing > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
