blast alignemnt query coverage

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6.7 years ago

sharmatina189059 ▴ 110

Can anyone tell me the error in this command. I want to get full query coverage also with my seq. alignment and when I am using qcovs it is showing error.

blastn -db 17978_old_complete_genome -query 17978new_ol_genes.fasta -perc_identity 90 -evalue 0.0001 -qcovs -outfmt 6  > complete_genome_0.0001_oneline_output_qcovs

blast • 4.0k views

ADD COMMENT • link updated 6.7 years ago by GouthamAtla 12k • written 6.7 years ago by sharmatina189059 ▴ 110

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Just try the same command with quotes The command string needs these quotes, such that the command line looks like:

blastn -outfmt "6 qcovs" ...

ADD REPLY • link 6.7 years ago by Karma ▴ 310

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Thanks ..it works but which coloumn gives query coverage

ADD REPLY • link 6.7 years ago by sharmatina189059 ▴ 110

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why don't you upload your results.. at-least first 10 lines

ADD REPLY • link 6.7 years ago by Karma ▴ 310

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Output should be in the same order as what you specified in -outfmt 6 "sseqid qseq qcovs sseq" gives you

gi|672239066|ref|NR_125655.1|   AACTGACAGTTTTAGAAACAGGACT   2   AATTGACAGTTTTAGAAATAGAACT
gi|631253076|ref|NR_114274.1|   AACTGACAGTTTTAGAAACAGGACT   2   AATTGACAGTTTTAGAAATAGAACT
gi|636560310|ref|NR_116370.1|   AACTGACAGTTTTAGAAACAGGACT   2   AATTGACAGTTTTAGAAATAGAACT
gi|343198619|ref|NR_043083.1|   CTAAAAGTTACCCCACCGAC    2   CTAAAGGTTACCCCACCGAC
gi|343201461|ref|NR_042187.1|   AACTGACAGTTTTAGAAACAGGACT   2   AATTGACAGTTTTAGAAATAGAACT

Here qcovs is in column 3.

ADD REPLY • link 6.7 years ago by GenoMax 141k

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Why don't you state the error that you are getting while running the command

ADD REPLY • link 6.7 years ago by Karma ▴ 310

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