Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : today
all time
today
this week
this month
this year
0 results • Page
1 of 1
Sort: replies
Rank
Views
Votes
Replies
Topic contains no posts.
No posts found.
0 results • Page
1 of 1
Recent Votes
STAR for bacterial genome
A: STAR for bacterial genome
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
How to interpret highly variable genes plot in Scanpy?
Comment: difference between target sequencing technologies
Comment: difference between target sequencing technologies
Comment: Problem using SRAtoolkit
Recent Locations •
All
Qatar,
1 minute ago
Israel,
3 minutes ago
India,
5 minutes ago
France,
5 minutes ago
Frankfurt Am Main,
6 minutes ago
United Kingdom,
7 minutes ago
United Kingdom,
7 minutes ago
Recent Awards •
All
Teacher
to
h.mon
34k
Popular Question
to
agata
▴ 10
Popular Question
to
yoosefyud
▴ 40
Popular Question
to
re_raz
▴ 40
Popular Question
to
Lucy
▴ 110
Teacher
to
ATpoint
68k
Popular Question
to
tianshenbio
▴ 160
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 …
Comment: Problem using SRAtoolkit
by
yoosefyud
▴ 40
Sure. Thanks for your help.
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. …
Traffic: 1010 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6