All right. Problem solved. The data showed up after I changed the seuqence reference in the bam file ....
samtools view -h SRR030765.bam > SRR030765.sam sed -i "s/NC_002754.1/chr/" SRR030765.sam samtools view -S -b SRR030765.sam > SRR030765-chr.bam ... did the trick. The reference was inserted by tophat, so now I'm looking for a way to tell tophat to insert a different reference. Bottom line: It's not a genome browser issue. Thanks for your suggestions! And thanks to the browser devs for creating and maintaining it! http://archaea.ucsc.edu/cgi-bin/hgTracks?org=Sulfolobus+solfataricus&position=chr%3A1-35000&hgt.customText=track%20type=bam%20name=xxxxxxxxxxxxxxxxxxxx%20bigDataUrl=http://rna-seqlyze-data.pfeifer.ch/custom-tracks/S.solfataricus/SRR030765-chr.bam http://x.vu/srr030765 On 2012-05-10 08:17, Patrick Pfeifer wrote: > Hello > > Thanks for your replies. > > I tried hosting this on galaxy as well, but that doesn't work either. > > https://main.g2.bx.psu.edu/u/dcgdftvcdv/h/bam-view > > I chacked the bam file using samscope (very nice find: > http://samscope.dna.bio.keio.ac.jp/wiki/index.php/Samscope) and the data > should be there: > http://rna-seqlyze-data.pfeifer.ch/various/SRR030765-2.bam.Samscope-screenshot.png > > Any other suggestions? > > > On 2012-05-10 01:06, Galt Barber wrote: >> We don't see any problems with the urls. >> curl -I on the .bam and .bam.bai show a good response. >> >> If you think that your bam is correct, >> try hosting it on some other http server and see >> if things improve. Actually, I tried this on >> your data and it did not help. >> >> Check the content of your bam. >> Even when we zoom out to the entire chromosome I don't see anything. >> >> The 200 and 206 calls are normal for bigDataUrl >> which access blocks of data. It often jumps to >> a position and resumes reading from there via >> byterange header request and the server responds >> with a 206. >> >> -Galt >> >> On 05/09/12 15:42, Hiram Clawson wrote: >>> Good Afternoon Patrick: >>> >>> The URL variable hgt.customText may work better if it is a URL >>> to a small file with your track definition line. To see examples >>> of this type of reference, note references from this page: >>> http://genome.ucsc.edu/goldenPath/customTracks/custTracks.html >>> >>> --Hiram >>> >>> >>> Patrick Pfeifer wrote: >>>> Hello >>>> >>>> I have a custom bam track with corresponding index (.bai) at >>>> >>>> http://rna-seqlyze-data.pfeifer.ch/custom-tracks/S.solfataricus/SRR030765-2.bam.bai >>>> >>>> You *should* be able to see it using this url: >>>> >>>> http://archaea.ucsc.edu/cgi-bin/hgTracks?org=Sulfolobus+solfataricus&position=chr%3A1-35000&hgt.customText=track%20type=bam%20name=xxxxxxxxxxxxxxxxxxxx%20bigDataUrl=http://rna-seqlyze-data.pfeifer.ch/custom-tracks/S.solfataricus/SRR030765-2.bam >>>> >>>> However, it does not work for some me for some reason. The track >>>> desription shows up in the browser and I see some HTTP HEAD & GET >>>> requests on my server, all with status 200 or 206, but there is no data >>>> visible in the browser. >>>> >>>> Can you give me any hints what I am doing wrong here? >>>> >>>> Thank you >>>> >>>> Patrick >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
