I just realized this list is configure with reply-to to the sender, I'm copying my answer of this email that I intended to send to the list. -- Carlos Javier Borroto Baltimore, MD
On Thu, Feb 24, 2011 at 1:05 PM, Carlos Javier Borroto <[email protected]> wrote: > On Thu, Feb 24, 2011 at 12:21 PM, Hiram Clawson <[email protected]> wrote: >> Good Morning Carlos: >> >> Here is an alternative procedure to create a coverage graph >> for a bam file: >> >> https://lists.soe.ucsc.edu/pipermail/genome/2010-December/024318.html >> > > I tried this, but is failing on Ubuntu Lucid: > samtools pileup mybam.sorted.bam | perl -pe '($c, $start, > undef, $depth) = split; \ > if ($c ne $lastC || $start != $lastStart+1) { \ > print "fixedStep chrom=chr$c start=$start step=1 > span=1\n"; \ > } \ > $_ = "$depth\n"; \ > ($lastC, $lastStart) = ($c, $start);' > syntax error at -e line 2, near "if" > syntax error at -e line 6, near ";}" > > My perl skills aren't that good, I even tried to move it to a file and > I got rid of the syntax error, but the script only prints the first > line. This is the file I created. > pileupToWiggle.pl: > > #!/usr/bin/perl > > ($c, $start, undef, $depth) = split; > if ($c ne $lastC || $start != $lastStart+1) { > print "fixedStep chrom=chr$c start=$start step=1 span=1\n"; > } > $_ = "$depth\n"; > ($lastC, $lastStart) = ($c, $start); > > And I tried to use it like this: > $ samtools pileup mybam.sorted.bam | pileupToWiggle.pl > fixedStep chrom=chr start= step=1 span=1 > > Would be nice to get it to work, any further help? > >> For assistance with BEDTools, please consult the bedTools project: >> http://code.google.com/p/bedtools/ >> > > I thought the problem could had been in the way I was declaring my > track, that there was an option to get it to display the data in the > way I wanted, but you are right, I should have gone to BEBTools > project website. > >> Can you intersect your graph with 'NOT gap' in the table browser >> to display the graph in areas that are not gap ? >> > > This I did not understand, I'm very new to the Genome Browser. > >> --Hiram > > Thanks for your comments, > -- > Carlos Javier Borroto > Baltimore, MD > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
