I think the issue may be with the bigBED format files we use in our search function. I am using the BED files which are in BED Details format, and using the bedToBigBed program to generate the bigBED files. The command I am using is (example):
grep -v track bed_detail.bed | sort -k1,1 -k2,2n > /tmp/tmp_bed_detail.bed bin/bedToBigBed -tabs -bedFields=9 -as=ISCA.as /tmp/tmp_bed_detail.bed hg18.chrom.sizes big_bed_detail.bb where ISCA.as is: table nstd37CustomTracks "ISCA Custom Tracks with NCBI variant ID and variant details link" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Feature start position" uint chromEnd; "Feature end position" string name; "CNV title" uint score; "Score" char[1] strand; "+ or - for strand" uint thickStart; "Color start position" uint thickEnd; "Color end position" string itemRGB; "Blue for duplication, Red for deletion" string variantID; "NCBI variant ID" string variantDetails; "html1" ) The output of bedToBigBed run on the ISCA_Uncertain track is shown: pass1 - making usageList (24 chroms): 2 millis pass2 - checking and writing primary data (2791 records, 11 fields): 20 millis index write: 0 millis pass3 - writeReducedOnceReturnReducedTwice: 5 millis further reductions: 2 millis I have attached an image of the error we are getting. Viren ________________________________ From: Vanessa Kirkup Swing [[email protected]] Sent: Tuesday, December 20, 2011 8:12 PM To: Patel, Viren Cc: [email protected] Subject: Re: [Genome] Error with ISCA custom tracks Hi Viren, We are unable to reproduce what you are describing. Can you please tell us all of the steps that led you to the Invalid signed integer error? Thanks! Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Patel, Viren <[email protected]<mailto:[email protected]>> Date: Tue, Dec 20, 2011 at 4:30 PM Subject: [Genome] Error with ISCA custom tracks To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Hello. We have previously generated custom tracks for ISCA CNV data (https://www.iscaconsortium.org/index.php/the-news/139-new-ucsc-tracks-now-available). Recently the Genome Browser has started giving an "Invalid signed integer" error when clicking on a CNV. We have not had any changes to the tracks and I am wondering if something may have changed in the Genome Browser custom tracks requirements. Please let me know what additional data you may need and how I can troubleshoot this issue. Thanks. Viren Patel www.iscaconsortium.org<http://www.iscaconsortium.org> ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments). _______________________________________________ Genome maillist - [email protected]<mailto:[email protected]> https://lists.soe.ucsc.edu/mailman/listinfo/genome
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