QA scripts

Shorthand Key:

file name		flnm
database name		dbnm
table name		tblnm

Scripts

catchBOT.csh		                    check usage of highest users
nice top		                    see who is doing what & the time on the server
up time			            load average
featureBits dbnm tblnm		            compares total amount of data in table compared to the entire assembly (not including gaps)
checkCoverage.csh dbnm tblnm [chrom]	    finds non-gap places in table where there is no data and gives you the largest places with browser link to top 3
findLevel.csh dbnm tblnm		    searches trackDb hierarchy for your table and corresponding .html file
commTrio.csh		                    sorts & compares two files
encodeEmail.pl		                    codes email addresses for html pages

countPerChrom.csh dbnm tblnm	            number of material on each chrom
countPerChrom.csh aplCal1 rmsk | awk '{ print $2 "\t" $1}' | grep '^0'
alternative: to see those chroms with data: hgsql -e "select tName from all_mrna;" aplCal1 | sort| uniq -c | sort -rn | less (per Hiram; more efficient)