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Get the secondary hists reads count from SAM awk '{ print $2 }' out.sam| grep "2048" | wc -l #SAM #BAM #Secondary #Hits

Find matching file names with pattern in a directory. $ ls -dq *_name2search_* | wc -l #file #search #hits #pattern #names #directory

Quickly #Finding #Orthologs as Reciprocal Best #Hits with #BLAT, #LAST, and #UBLAST: How Much Do We Miss? http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0101850