Question: sorting blast results by sseq coverage
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3 months ago
nheb1977 • 0

my query blastn search returns - 3 sequences tie ( subject sequence) with identical score , e-value and alignment length.

These 3 sequences are of different length. Is there any way to output results so that the hit with highest subject sequence coverage (or in other words, the shortest hit) is displayed first?

ADD COMMENTlink 3 months ago nheb1977 • 0
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Hi nheb1977,

Try adding -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore slen" when running BLAST, then sort the results using sort -k1,1 -k12,12nr -k11,11n -k4,4nr -k13,13n.

ADD REPLYlink 3 months ago
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