Good afternoon, I'd been trying to figure out how to build a simple script to query several intervals at once using bigWigToWig and print the results into a file.
For example: Instead of having the following lines that print separate files, ... bigWigToWig -chrom=chr1 -start=1000 -end=1010 http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeBuOrchidV1.bigWig qry1.txt bigWigToWig -chrom=chr2 -start=2000 -end=2010 http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeBuOrchidV1.bigWig qry2.txt bigWigToWig -chrom=chr3 -start=3000 -end=3010 http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeBuOrchidV1.bigWig qry3.txt ... I would like to have the same queries in a single script that print into a single file. Many thanks again, Regards, Diego -----Original Message----- From: Hiram Clawson [mailto:[email protected]] Sent: Thursday, December 01, 2011 7:26 PM To: Diego Pereira Cc: [email protected] Subject: Re: [Genome] Hg19 tables You need to look where there is actual data. You can find locations for data by looking at the tracks in the genome browser. Or asking for a larger interval: $ bigWigToWig -chrom=chr1 -start=1000 -end=10010 http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeBuOrchidV1.bigWig stdout variableStep chrom=chr1 span=1 10004 0.4125 10005 -0.18625 10006 0.11225 10007 0.26725 10008 -0.06475 10009 0.11 10010 0.4125 $ bigWigToBedGraph -chrom=chr1 -start=1000 -end=10010 http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeBuOrchidV1.bigWig stdout chr1 10003 10004 0.4125 chr1 10004 10005 -0.18625 chr1 10005 10006 0.11225 chr1 10006 10007 0.26725 chr1 10007 10008 -0.06475 chr1 10008 10009 0.11 chr1 10009 10010 0.4125 $ bigWigInfo -chroms http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeBuOrchidV1.bigWig version: 4 isCompressed: yes isSwapped: 0 primaryDataSize: 14,289,996,669 primaryIndexSize: 89,736,320 zoomLevels: 10 chromCount: 24 chr1 0 249250621 chr10 1 135534747 chr11 2 135006516 chr12 3 133851895 chr13 4 115169878 chr14 5 107349540 chr15 6 102531392 chr16 7 90354753 chr17 8 81195210 chr18 9 78077248 chr19 10 59128983 chr2 11 243199373 chr20 12 63025520 chr21 13 48129895 chr22 14 51304566 chr3 15 198022430 chr4 16 191154276 chr5 17 180915260 chr6 18 171115067 chr7 19 159138663 chr8 20 146364022 chr9 21 141213431 chrX 22 155270560 chrY 23 59373566 basesCovered: 2,861,325,143 mean: 0.265295 min: -0.790750 max: 1.644750 std: 0.480838 $ bigWigSummary http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeBuOrchidV1.bigWig chr1 1000 10010 1 0.384723 Diego Pereira wrote: > Good afternoon Hiram, > > I tried the following and some variations but I couldn't make it work. > > bigWigToWig > http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeBuOrchidV1.bigWig > -chrom=chr1 > -start=1000 -end=1010 > > May I ask you to write it down correctly? > > Many thanks, _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
