The wiki page had a typographical error: the $ sign should not be there in the chainNet command. I have fixed the wiki page.
Also, I don't think chainNet will take a wildcard like *.chain as its first parameter, unless you only have one .chain file. -Galt On 08/01/11 13:14, Vanessa Kirkup Swing wrote: > Hi Tejashwari, > > Is this the part where you are stuck on? > > > [makon@phorest chain]$ chain Merge Sort > > bash: chain: command not found > > > If so, the reason that command wasn't working was because you had spaces: > > chain Merge Sort > > when it should be: > > chainMergeSort > > > If you continue to have problems, please contact the mailing list: > [email protected]. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > > > > ---------- Forwarded message ---------- > From: Tejashwari Meerupati <[email protected]> > Date: Thu, Jul 28, 2011 at 1:57 AM > Subject: [Genome] command not working in UCSC minimal steps for liftover > To: "[email protected]" <[email protected]> > Cc: "[email protected]" <[email protected]> > > > > Dear Sir/Madam, > > My name is Tejashwari, PhD student at the Department of Microbial > Ecology, Lund University, Sweden. > I am working with the UCSC minimal steps for liftover (since i have > two different assemblies of the same organism). I had completed upto > step 5 chainMergesort (combine and sort chain files from [4]. > but from the step 6 (i.e) make alignment nets from chains in [5]. > > I used the following command and I get no output but ... > below pasted the command that I had been using: > > ********************************************************************************** > > [teju@phorest chain]$ chainNet *.chain > /home/teju/teju_2/chrom/tworuns_chromsizes > /home/teju/teju_2/chrom/pairend_chromsizes $ ../net/chr.net /dev/null > chainNet - Make alignment nets out of chains > usage: > chainNet in.chain target.sizes query.sizes target.net query.net > where: > in.chain is the chain file sorted by score > target.sizes contains the size of the target sequences > query.sizes contains the size of the query sequences > target.net is the output over the target genome > query.net is the output over the query genome > options: > -minSpace=N - minimum gap size to fill, default 25 > -minFill=N - default half of minSpace > -minScore=N - minimum chain score to consider, default 2000.0 > -verbose=N - Alter verbosity (default 1) > -inclHap - include query sequences name in the form *_hap*. Normally > these are excluded from nets as being haplotype > pseudochromosomes > > [makon@phorest chain]$ chain Merge Sort > bash: chain: command not found > [makon@phorest chain]$ chainMergeSort > chainMergeSort - Combine sorted files into larger sorted file > usage: > chainMergeSort file(s) > Output goes to standard output > options: > -saveId - keep the existing chain ids. > -inputList=somefile - somefile contains list of input chain files. > -tempDir=somedir/ - somedir has space for temporary sorting data, default ./ > > > even i tried with different options mentioned in chain net but dosent work. > > Can you kindly tell me what ould be the problem? > > Many thanks in advance. > > Sincerely > Tejashwari > > > ************************* > Tejashwari Meerupati > PhD Student > Department of Microbial Ecology > Lund University > SE - 223 62, Lund > Sweden > E - mail: [email protected] > ************************* > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
