Thank you Brooke. Regards,
Diego -----Original Message----- From: Brooke Rhead [mailto:[email protected]] Sent: Friday, December 02, 2011 6:45 PM To: Diego F. Pereira Cc: [email protected] Subject: Re: [Genome] Hg19 tables Hi Diego, This is beyond the scope of the help we are able to provide via the Genome Browser mailing list. I suggest finding a collaborator familiar with shell scripting to help you further. Good luck with your research! -- Brooke Rhead UCSC Genome Bioinformatics Group On 12/2/11 2:46 PM, Diego F. Pereira wrote: > 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.bigWi >> g >> -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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
