User: maximilian.mayerhofer

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New User
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Last seen:
11 months ago
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1 year, 1 month ago
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m********************@gmx.net

Posts by maximilian.mayerhofer

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Virtual Alignment program?
... Of course, my question is: is there a pipeline/program that can do that for me? Or do I have to do this by hand? ...
written 11 months ago by maximilian.mayerhofer20
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Virtual Alignment program?
... Hello, I need to do an alignment like in the picture ![alignment][1] Is there a way to do that automatically ? Currently, I am using MAFFT to align the sequences and then Jalview to view them - do you know of a program to produce alignments like this? Best regards [1]: https://www.researchg ...
sequence alignment written 11 months ago by maximilian.mayerhofer20
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Answer: A: Blast Output not in correct dir
... So, since that seemed to be a bug, I used the following workaround: blastn -query $F -db ../database/blastdb/dbGOI.fasta -outfmt 5 >> ../output/results.xml since I used cat to put all theoutput files together, I save a line of code. ...
written 11 months ago by maximilian.mayerhofer20
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Comment: C: Blast Output not in correct dir
... Jep, I tried full path, relative path or no path at all but everytime ( also with no specific path) it gets put into the genomes dir. ...
written 11 months ago by maximilian.mayerhofer20
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Comment: C: Blast Output not in correct dir
... even with the ".." it isnt outputting it correctly. ...
written 11 months ago by maximilian.mayerhofer20
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Comment: C: Blast Output not in correct dir
... problem is, even if I am in the script dir, the blast result are put into the genomes dir and not in the output dir. ...
written 11 months ago by maximilian.mayerhofer20
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Comment: C: Blast Output not in correct dir
... -out ../output/${F%.*}.xml but this says, go one folder above, into output and put it there? ...
written 11 months ago by maximilian.mayerhofer20
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Blast Output not in correct dir
... So, I have a directory: Pipeline - database: contains the custom blast database - scripts - genomes - output I want my local blast.sh script ( in the script folder) to take all the *.fna of the genomes folder and put results in the output folder. So i specified the following: for F in . ...
blast written 11 months ago by maximilian.mayerhofer20
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How to determine seq technology used in genome assembly?
... How do I determine the used sequence technology of a published genome? For example: I have the list of all available genomes of L. pneumophilia (https://www.ncbi.nlm.nih.gov/genome/genomes/416 ) If I click on one strain (https://www.ncbi.nlm.nih.gov/assembly/GCA_001752885.1#/st) It should be listet ...
bioinformatics sequencing written 11 months ago by maximilian.mayerhofer20 • updated 11 months ago by genomax63k
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Answer: A: Aligning Protein Seq multifasta
... Update: I used the wrong translation table, therefor, the translation was flawed. After correction, mafft was useful again. ...
written 12 months ago by maximilian.mayerhofer20

Latest awards to maximilian.mayerhofer

Scholar 11 months ago, created an answer that has been accepted. For A: Extracting specific IDs + sequence from multifasta
Scholar 12 months ago, created an answer that has been accepted. For A: Extracting specific IDs + sequence from multifasta
Scholar 13 months ago, created an answer that has been accepted. For A: Extracting specific IDs + sequence from multifasta

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