User: 6schulte
6schulte • 20
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- 11 hours ago
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- 2 months, 1 week ago
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- 6*******@informatik.uni-hamburg.de
Posts by 6schulte
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1
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Comment:
A: Make tblastn run faster
... Maybe you are requesting your computer to do too many threads when multi-threading? I have had the issue on my VM. I thought I had allowed the VM to work on 4 but in reality it was only 3. This led to such error messages for me, when I wanted to run four processes simultaneously... ...
written 3 days ago by
6schulte • 20
1
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... If anybody comes across this in the future:
I have compared the successrate of the three `-org` modes interesting for me: Archaea: `'arch'`, Gram-positive: `'gram+'`, Gram-negative: `'gram-'`.
The result showed that there is '**no significant difference**' (0) in success of finding/ identifying a ...
written 3 days ago by
6schulte • 20
0
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1
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71
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... My previous version was only `half way` functioning:
This
awk '/[a-zA-Z][a-zA-Z][a-zA-Z_][0-9][0-9][0-9][0-9][0-9]*\t[a-zA-Z][a-zA-Z][a-zA-Z_][0-9][0-9][0-9][0-9][0-9]*/{ print NR; exit }' $2 > number
tells me in which line two acc. no. occur after one another.
In my case it is in the sec ...
written 4 days ago by
6schulte • 20
1
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1
answer
71
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... I have a `solution`:
number=$(awk '/[a-zA-Z][a-zA-Z][a-zA-Z_][0-9][0-9][0-9][0-9][0-9]*\t[a-zA-Z][a-zA-Z][a-zA-Z_][0-9][0-9][0-9][0-9][0-9]*/{ print NR; exit }' $2)
sed -e "$number s/\t/\n/" $2 > text_test
This can run in a `loop`. ...
written 4 days ago by
6schulte • 20
0
votes
1
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71
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... I also thought about approaching this by using `awk` and checking if there is content in a fourth column.
-> If everything goes right the file should have three entries for each line, `separated by a tab`.
In the case of `two consecutive acc. no.` we have four entries for that line, therefore ...
written 4 days ago by
6schulte • 20
2
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1
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71
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1
answer
... I have a table that I fill with taxonomy information. This information I am requesting from `NCBI` using `efetch`. How I do it is described here: https://www.biostars.org/p/474001/#474629.
Now I want to use a bash-line command to `find two consecutive accession numbers`. They should not appear but ...
written 4 days ago by
6schulte • 20
6
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2
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115
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... Hello,
Has anyone an idea of wether there is some link to a `website` telling me `how many sequences` (as in entries) are currently to be found in the `non redundant database` of NCBI (nr.gz from [NCBI][1])?
I know I can let a `bash-line` command run through the downloaded and unpacked db and coun ...
written 19 days ago by
6schulte • 20
0
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2
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22k
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2
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Comment:
C: nr- protein database
... Hi,
I know this question is rater old but maybe someone will be needing this information anyways:
Use epost and esummary (NCBIs eutils) to obtain information on the lineage.
Something like this could help:
cat "$ListWithAccessionNumbers" | epost -db protein |\
esummary -db taxonomy -for ...
written 19 days ago by
6schulte • 20
0
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1
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120
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... Yes, I fears so too.
My supervisor suggested otherwise but the documentation doesn't give any indications for this assumption so I will run a little `test` and see `which of the two options finds the most signal peptides`. If no significant difference between the two is found I will have to run it t ...
written 5 weeks ago by
6schulte • 20
1
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2
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172
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... Thank you for this comment! I will get right to it. ...
written 5 weeks ago by
6schulte • 20
Latest awards to 6schulte
Scholar
3 days ago,
created an answer that has been accepted.
For A: bash find consecutive acc. no. & insert text
Scholar
4 days ago,
created an answer that has been accepted.
For A: bash find consecutive acc. no. & insert text
Supporter
11 days ago,
voted at least 25 times.
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