blast alignemnt query coverage
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
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GouthamAtla
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sharmatina189059 •
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sharmatina189059 •
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Why don't you state the error that you are getting while running the command
The pattern of somehow receiving upvotes for trivial comments continues into your new account, Mask/snijesh. If you're encouraging your colleagues to do this, as you mentioned in your previous comments, please do not do that. If not, I direct this message to the OP sharmatina189059 and ask them to use upvotes with caution and award them to posts that contribute significantly to the subject matter at hand.
I am not sure what you are worried about. I did not tell anyone to upvote my comments.
Not to debate semantics, but I'm not "worried" about anything.
You remarked on how Mask was your previous account (See: C: RNA-Seq or Exome Seq for Clinical data analysis ). Using the older account, you also said you'd asked your colleagues to up-vote your comments. (See: C: Getting error in running GATK (GenomeAnalysisTK-3.7)? ), which we observed as odd owing to them being up-votes to relatively trivial comments.
Here, the pattern of receiving up-votes to trivial comments continues, so I asked you if your colleagues were still doing this, or if this were a one-off occurrence (a possibility I addressed with the comment directed to /u/sharmatina189059 ).
I hope this clears stuff up for you.
I am not using the account you mentioned and I don't know who upvoted my comments here.
Thank you for clearing that up. New users tend to upvote any response they get, so that might be the case here.
If that is the case, can you remove those
unwanted commentsfrom the sectionsJust try the same command with quotes The command string needs these quotes, such that the command line looks like:
Thanks ..it works but which coloumn gives query coverage
why don't you upload your results.. at-least first 10 lines
Output should be in the same order as what you specified in
-outfmt 6 "sseqid qseq qcovs sseq"gives youHere
qcovsis in column 3.