Entering edit mode
12.8 years ago
Gireesh K. Bogu
▴
100
I often fail to upload very big wiggle files into UCSC browser so I end up uploading them into IGV. I am just wondering is there any fastest way of uploading wiggle file into UCSC browser ? If the file is too big I am ending up with this error "needMem: trying to allocate 1607029065 bytes (limit: 500000000)". I would like to hear what is the best and fastest way of uploading a wiggle file or multiple wiggle files (at the same time) into UCSC browser.
Thanx!
Yes. Thanx. I totally missed this article about buigWig. http://bioinformatics.oxfordjournals.org/content/26/17/2204.full . However, I am unable to upload my bedGraph files or bigWig files into UCSC. I created these by using the following 2 commands using Kent tools. (1) sort -k1,1 -k2,2n R15.bed | ./bedItemOverlapCount hg19 -chromSize=hg19.chromsizes stdin >>R15.bg (2nd command) bedGraphToBigWig R15.bg hg19.chromsizes R15.bw
Yes. Thanx. I totally missed this article about bigWig. bioinformatics.oxfordjournals.org/content/26/17/… . However, I am unable to upload my bedGraph files or bigWig files into UCSC. I created these by using the following 2 commands using Kent tools. (1) sort -k1,1 -k2,2n R15.bed | ./bedItemOverlapCount hg19 -chromSize=hg19.chromsizes stdin >>R15.bg (2nd command) bedGraphToBigWig R15.bg hg19.chromsizes R15.bw – Gireesh K. Bogu 0 secs ago
Yes. Thanx. I totally missed this article about bigWig ("BigWig and BigBed: enabling browsing of large distributed datasets"). However, I am unable to upload my bedGraph files or bigWig files into UCSC. I created these by using the following 2 commands using Kent tools. (1) sort -k1,1 -k2,2n R15.bed | ./bedItemOverlapCount hg19 -chromSize=hg19.chromsizes stdin >>R15.bg (2nd command) bedGraphToBigWig R15.bg hg19.chromsizes R15.bw – Gireesh K. Bogu 0 secs ago
Yes. Thanx. I totally missed this article about bigWig ("BigWig and BigBed: enabling browsing of large distributed datasets")