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Recent Replies
Comment: blastn (Error: Too many positional arguments (1))
by
GenoMax
125k
Use the following to check the database.
$ blastdbcheck -h
USAGE
blastdbcheck [-h] [-help] [-db DbName] [-dbtype mo…
Comment: How to interpret highly variable genes plot in Scanpy?
by
mt_pereira
•
0
Hello! I am going through scanpy and have the same doubt. Have you reached a conclusion on how to interpret the data presented by these gra…
Comment: blastn (Error: Too many positional arguments (1))
by
agata
▴
10
Thank you for suggestion!
Unfortunately, it still does not work... I have checked one more time my database with `blastcmd` and it works f…
Comment: difference between target sequencing technologies
by
pingu77
▴
10
Thanks a lot for your help!
Comment: blastn (Error: Too many positional arguments (1))
by
GenoMax
125k
> without nt in -db it creates only an empty result file
Then your databases are likely not created properly. If you are creating a databa…
Comment: blastn (Error: Too many positional arguments (1))
by
agata
▴
10
I'm not sure if following completely; It's not a basename, but together with `.fna` are different files produced by `makeblastdb`; my `$QUE…
Answer: A Computer Scientist who wants to start Bioinformatics
by
omaridris5315
•
0
I saw some introductory course on coursera which is one hour work and includes processing NSG data, blast and Galaxy formats. I am interest…
Comment: Problem using SRAtoolkit
by
GenoMax
125k
If you are sure the files are in `.sra` format then you could rename one file and try. Something like
mv file file.sra
fastq-dump …
Answer: blastn (Error: Too many positional arguments (1))
by
GenoMax
125k
blastn -db nt $DATABASE_DIR/$GCA/$GCA.fna -query $QUERY -out $file_out -num_threads $CPU -outfmt "6 qseqid sseqid sstart send evalue le…
Comment: Problem using SRAtoolkit
by
GenoMax
125k
Try processing one file and see it works before you try the loop. In case your files are corrupt this is not going to work.
Comment: Problem using SRAtoolkit
by
yoosefyud
▴
40
No. I downloaded them by clicking on download link in NCBI website.
Comment: Problem using SRAtoolkit
by
GenoMax
125k
Did you download the files from SRA using `prefetch`?
Comment: Problem using SRAtoolkit
by
yoosefyud
▴
40
Thanks for your help. Actually I was trying to use following loop to split my SRA files. However, I think the problem relates to my file ex…
Answer: Problem using SRAtoolkit
by
GenoMax
125k
Message tells you what you need to do. You need to provide an SRA accession number or name of a downloaded `.sra` file with this command.
…
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