Hello Gerardo, It's really really helpful for my research! Thank you so much! Thanks again for building such a nice platform and providing so much

php/DoBlastzChainNet.pl#The_new_streamline_pairLastz_script >>> at the step of running DoBlastzChainNet.pl. ( I used localhost instead >>> of other host

> the doBlastzChainNet.pl. However,the program have not run successfully on > my server. Then I have used Lastz and got the alignment file (figure 1). > When I compare it with

title=DoBlastzChainNet.pl. If you have any further questions, please reply to genome@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google

php/DoBlastzChainNet.pl. > > > > All steps ran quickly except for the last step "chainStitchId" which > failed with an error. > > > > Here is

pipeline(DoBlastzChainNet.pl - genomewiki (ucsc.edu)) and run the task successfully.My script is as follows: > > export PATH="/storage/reference/13.cross.species

in the DoBlastzChainNet.pl wiki. One of our engineers shares that the nextflow appears to do the same procedure and it would be fine to use the nextflow procedure instead of our workflow

using the DoBlastzChainNet.pl script that can be found on the following wiki page: https://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl You can see an example of the script

DoSameSpeciesLiftOver.pl from BLAT alignments > 2) hg38ToHs1.over.chain.gz was generated by UCSC using DoBlastzChainNet.pl > from LASTZ alignments > 3) hg38-chm13v2

have the doBlastzChainNet.pl script/process which was used to create the hg19 to mm9 liftOver chain file: https://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl. The

php/DoBlastzChainNet.pl#lastz_parameter_file http://genomewiki.ucsc.edu/index.php/Lastz_DEF_file_parameters You can also review the following makedocs for some example

used the doBlastzChainNet.pl script with the lastz parameters since it tends to do better for human-rodent distances or greater. We offer some example lastz parameters on the following

myself using doBlastzChainNet.pl > but that doesn't seems to be the recommended way. > > Thanks in advance, > Regards, > Fabien Sassolas, PhD student @IGFL >

partitionSequence.pl 32100000 10000 /gpfs/scratch/withomas/project_noRoot_MGA/data/genomes/dm6/dm6.2bit /gpfs/scratch/withomas/project_noRoot_MGA/data/genomes

php/DoBlastzChainNet.pl > > It seems that some of the software at that latter link is specific to the architecture on your > system, however. For example, the [Parasol Job

mention of doBlastzChainNet.pl that would be useful to review: https://groups.google.com/a/soe.ucsc.edu/g/genome/search?q=doBlastzChainNet.pl Thank you again for your

php/DoBlastzChainNet.pl This describes the process of using our scripting tool chain that performs a whole genome alignment. You can view the actual script in our source tree: https

at the doBlastzChainNet.pl, it looks like you proceed in the following way: > > 1. Align with blastz with proper parameters and save as lav > 2. Convert to psl with lavToAxt

php/DoBlastzChainNet.pl): - *DoBlastzChainNet.pl* - which is focused on creating chains between two assemblies from different organisms (eg mouse mm10 and human hg38) - This answer

: - DoBlastzChainNet.pl - which is focused on creating chains between two assemblies from different organisms (eg mouse mm10 and human hg38) - If this is what you're after, then

: - DoBlastzChainNet.pl - which is focused on creating chains between two assemblies from different organisms (eg mouse mm10 and human hg38) - If this is what you're after, then

constructLiftFile.pl is different to other fragments. I changed the constructLiftFile.pl and solved this problem, but other chromosomes (such as chr4) arised the same problem

. The doBlastzChainNet.pl script will create a pairwise alignment and the lastz parameters are defined inside a DEF file. Some example lastz parameters used for human can be found

doBlatzChainsNets.pl, which requires 2bit and chrom.sizes input files. Generating these will require two additional utilities "faToTwoBit" and "faSizes -detailed

php/DoBlastzChainNet.pl Once you have your pairwise MAF files made, you will need to run the MultiZ program to generate multi-species MAF files. For a reference on how a 5-way MultiZ

with the doBlastzChainNet.pl script, producing pairwise MAF files 2. Collect those pairwise-MAF files in one place, run MultiZ to produce a multi-species MAF file 3. Visualize that

DoSameSpeciesLiftOver.pl) and a second for more general liftOver chains ( http://genomewiki.ucsc.edu/index.php/DoBlastzChainNet.pl). If you have issues throughout the process

DoSameSpeciesLiftOver.pl Unfortunately, it is beyond the scope of this mailing list to provide scientific advice such as the lastz parameters to use to generate your alignments

php/DoBlastzChainNet.pl Please let us know if you have any further questions! Thanks, Christopher Lee UCSC Genomics Institute On Wed, Sep 12, 2018 at 3:44 AM, Shuai Dominique Ding

php/DoBlastzChainNet.pl Our makeDb/doc/* files have many examples of how to run multiz and phastCons on a few species. For example, bosTau4.txt shows the steps that one of our engineers