ucscGenomeBrowser
Question about classNet
Hello,
This bug appeared when I was running netClass，“can't find mysql connection info for database GCF_000001405.40_GRCh38.p14_genomic.fna in hg.conf or ~/.hg.conf, should have a default profile named "db", so values for at least db.host, db.user and db.password. See http://genomewiki.ucsc.edu/index.php/Hg.conf”. And I don't know what "tDb and qDb" are, could you tell me?
Do I need to set qRepeats and tRepeats? Something like the following figure.Or can I run netSyntenic and go straight to netfilter and skip this step?
Best regards, Hao
Good Evening Marh32: Running the 'netClass' command expects to find repeat information about your query and target genomes in database tables. Run the 'netClass' command without any arguments to see a description of what tDb and qDb are referring to. I'm very curious what procedure you may be running that got you to 'netClass' ? If you do not have databases for the genomes you are using, you don't need to run netClass, you can use your noClass.net file directly without that extra information: netFilter -minGap=10 noClass.net | hgLoadNet -test -noBin -warn -verbose=0 $tDb net$QDb stdin.
Thank you so much for your reply. I was processing the results of a lastz run with pairwise alignment, and then ran axtchain, chainPreNet, chainNet, and netSyntenic, but after running netClass the above error occurred, and here is the command I entered: netClass -noAr noclass.net GCF_000001405.40_GRCh38.p14_genomic.fna GCF_000164805.1_Tarsius_syrichta-2.0.1_genomic.fna class.net,I want to continue with multiz and phastcons to identify conserved elements in the genomes.
tDb - database to fetch target repeat masker table information,I would also like to ask you about the specific format of database.Thank you very much
The database tables are the repeatMasker tables rmsk in the UCSC browser database system. You can access these databases with the public MySQL server: http://genome.ucsc.edu/goldenPath/help/mysql.html I'm assuming you are reproducing the primate chains and nets: genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=primateChainNet. https://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsTarSyr2/
Yes，I'm reproducing the primate chains and nets.So if I want to complete the chains and nets step according to my own sequencing data, can I skip the netClass step and directly run netFilter with –syn flag (then do multiz and phastcons)? I see that you have also run reciprocal best, is this step also realized through netFilter? Or do you have a specific process? I didn't find a detailed description on the uscs browser and was a bit confused Thank you very much for your answer.
https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/utils/automation/doRecipBest.pl
It isn't necessary to make all the different net files. Only one type is used in the multiple alignment depending upon the distance between the genomes. https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/hg38/multiz30way.txt