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
