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:
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[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
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Tejashwari Meerupati
PhD Student
Department of Microbial Ecology
Lund University
SE - 223 62, Lund
Sweden
E - mail: [email protected]
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