User: 6schulte

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6schulte20
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2 months, 1 week ago
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Posts by 6schulte

<prev • 21 results • page 1 of 3 • next >
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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 6schulte20
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Answer: A: SignalP - choosing the right organism
... 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 6schulte20
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Comment: C: bash find consecutive acc. no. & insert text
... 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 }' $2 > number tells me in which line two acc. no. occur after one another. In my case it is in the sec ...
written 4 days ago by 6schulte20
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Answer: A: bash find consecutive acc. no. & insert text
... I have a `solution`: number=$(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/" $2 > text_test This can run in a `loop`. ...
written 4 days ago by 6schulte20
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Comment: C: bash find consecutive acc. no. & insert text
... I also thought about approaching this by using `awk` and checking if there is content in a fourth column. -> If everything goes right the file should have three entries for each line, `separated by a tab`. In the case of `two consecutive acc. no.` we have four entries for that line, therefore ...
written 4 days ago by 6schulte20
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bash find consecutive acc. no. & insert text
... I have a table that I fill with taxonomy information. This information I am requesting from `NCBI` using `efetch`. How I do it is described here: https://www.biostars.org/p/474001/#474629. Now I want to use a bash-line command to `find two consecutive accession numbers`. They should not appear but ...
ncbi efetch bash acc.no. written 4 days ago by 6schulte20
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Number of Entries in Non Redundant DB
... Hello, Has anyone an idea of wether there is some link to a `website` telling me `how many sequences` (as in entries) are currently to be found in the `non redundant database` of NCBI (nr.gz from [NCBI][1])? I know I can let a `bash-line` command run through the downloaded and unpacked db and coun ...
ncbi nr written 19 days ago by 6schulte20
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Comment: C: nr- protein database
... Hi, I know this question is rater old but maybe someone will be needing this information anyways: Use epost and esummary (NCBIs eutils) to obtain information on the lineage. Something like this could help: cat "$ListWithAccessionNumbers" | epost -db protein |\ esummary -db taxonomy -for ...
written 19 days ago by 6schulte20
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Comment: C: SignalP - choosing the right organism
... 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 6schulte20
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Comment: C: How to extract header from within the data (line of a file)
... Thank you for this comment! I will get right to it. ...
written 5 weeks ago by 6schulte20

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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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