I found a solution for reasonably small tracks (as known genes, refseq, ensembl genes and such):
1. create Base-pair-wise intersection and submit it as custom track to Table browser; 2. download such track not as bed (it will not work either, still creating truncated file) but as all fields from a table (resulting file is a bed track with a few commented lines). However, this solution does not work for large tracks like for example dbSNP129. Just can not get Base-pair-wise self-intersection for snp129 even in table browser. I know that getting bed file for dbSNP129 self-intersect directly from Table browser worked as last year September (I still have the file). Lucky me - seems like dbSNP129 table was not updated since that time so I may use last year download. But the question is still the same: if now I can not use table browser for Base-pair-wise intersection - what would you recommend me to get this? Thanks a lot! Irina ________________________________ From: Khrebtukova, Irina Sent: Sunday, May 03, 2009 9:54 AM To: '[email protected]' Subject: local Base-pair-wise intersection I'm trying to use Table browser to get BED tracks of Base-pair-wise intersection of various tracks. For example, intersecting dbSNP and knownGene exons to get a track of genome bases in dbSNP covered by any known genes exon. This used to work for any track but now it works for small tracks only. Even intersecting known gene track to itself to get bed track of genome bases covered by known genes exons does not work any more - the file is truncated: $ tail knownGenes_bitwiseIntersect chr11 95160435 95160490 chr11.9285 chr11 95161310 95161375 chr11.9286 chr11 95162203 95162602 chr11.9287 chr11 95163289 95163555 chr11.9288 chr11 95172043 95172200 chr11.9289 chr11 95185715 95185923 chr11.9290 chr11 95186279 95186401 chr11.9291 ------------------------------------------------------------------------ --- Allocated too much memory - more than 6,442,450,941 bytes (6,442,483,623) ------------------------------------------------------------------------ --- Is it possible for me to do such intersection locally? I mean without setting up whole local browser. Or may be you can suggest some other way around. Thanks! Irina Khrebtukova, PhD Sr. Staff Bioinformatics Scientist Gene Expression Applications R&D Illumina Inc. 25861 Industrial Blvd., Hayward, CA 94545 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
