I'm trying to add custom tracks to a UCSC genome browser session. I can add BAM files as follows:
track type=bam name="bam1" bigDataUrl=http://...bam1.bam
This works and UCSC is able to retrieve the BAM file and display it as a track. I'd like to also include BED files as tracks as well. I tried adding it to the custom tracks file like this:
track type=bam name="bam1" bigDataUrl=http://...bam1.bam
track name="bed1" url=http://...bed1.bed
But it complains about the second (BED) line. If I add type=bed
to the second line after track
it still does not work. How can I tell UCSC the locations of multiple BAM and BED files and have it load those as separate tracks? thanks
What is
bed1.bam
, either its bed or bam. Also check Visualizing Chip-Seq Data Using Ucsc [Bigwig]Sorry, typo, it's meant to be a .bed
Try converting
bed
tobigbed
using bedToBigBed and replace theurl
withbigDataUrl
. It should work, I am not sure, If ucsc picks up bed file and anyways why to send a heavy file when you can use small, light weight encrypted formats (bigBed
,bigwig
etc.)I am running it locally so file size is not an issue. When I try it as bedGraph with the following line:
track type=bedGraph name="mytrack" bigDataUrl=theurl
I get the error
"Unrecognized format type=bedGraph line 2 of custom track"
. Very frustrating, I follow the same exact syntax they show in the exampleThat error probably means that the line does not start with "chr". UCSC bedGraph requires only chromosomes 1-22, X, Y and M prefixed with "chr".
Sukhdeep Singh's response below is correct. The reason for this error is that bedGraph is not a valid bigDataUrl file format. As far as I can tell, bedGraph format can only be specified by adding "track type=bedGraph" in the track definition line of the bedGraph file itself, i.e. bedGraph cannot be specified as a type in the "Paste URLs or data:" box on the UCSC Add Custom Tracks page. If "track type=bedGraph" is not added to a bedGraph file, it is interpreted by the browser simply as a plain bed file with column 4 (the quantitative value) used as the bed interval name.