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Results for "hits"

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• • Marysia@marysia

  

  How to print only the first best hit from blastn tool?

  I used the following command to print the blast hit. [Terminal] blastn -query aaa.fa -db blastdb/nt -evalue 10e-5 -num_threads 4 -max_target_seqs 1 -outfmt '6 qseqid staxid qstart qend sallseqi sstart send evalue length frames qcovs' -out testBlastSee But the outfile print many hits, I only...

  Tags: blastn, blastall, megablast, top, hits

  2612 days ago

• • Jit@jit.aber

  

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

  Tags: file, search, hits, pattern, names, directory

  2229 days ago

• • Jit@jit.aber

  

  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

  Tags: Finding, Orthologs, Hits, BLAT, LAST, UBLAST

  2537 days ago

• • Jit@jit.aber

  

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

  Tags: SAM, BAM, Secondary, Hits

  1828 days ago

• • Shruti Paniwala@shruti

  

  CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R

  CRBHits is a coding sequence (CDS) analysis pipeline in R (R Core Team, 2019). It reimplements the Conditional Reciprocal Best Hit (CRBH) algorithm crb-blast and covers all necessary steps from sequence similarity searches, codon alignments to Ka/Ks calculations and synteny. The new R package tar...

  Tags: CRBHits, Conditional, Reciprocal, Best, Hits, Codon, Alignments, Ka/Ks, R

  1262 days ago