for blastp output

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7.5 years ago

bandanaschapagain ▴ 30

Hie, I am very new to bioinformatic and I need help for this- I am using blastp to align my sequence for my blastp command I am using blastp -db protein_dir.db -query GCF_000008785.1_ASM878v1_protein.faa.out_sp.out.daa.m8.hits_orfans_result_final_n0_l_seq -out test -outfmt "6 qcovs" but I am not getting column 12 with query coverage any how. I hope to hear soon

RNA-Seq alignment • 2.2k views

ADD COMMENT • link updated 7.5 years ago by WouterDeCoster 47k • written 7.5 years ago by bandanaschapagain ▴ 30

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As far as I remember, the column 12 in this format is bitscore. You may try -outfmt ' 6 std qcovs'.

ADD REPLY • link 7.5 years ago by seta ★ 1.9k

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I used the above provided option but still I not getting querycov.I am counting column 12 as starting from zero.. Can anyone help me with this I am trying aloot to figure it out Thanx

ADD REPLY • link 7.5 years ago by bandanaschapagain ▴ 30

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