User: maximilian.mayerhofer

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6 months ago
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8 months, 1 week 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 6 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 6 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 $F -db ../database/blastdb/dbGOI.fasta -outfmt 5 >> ../output/results.xml since I used cat to put all theoutput files together, I save a line of code. ...
written 6 months ago by maximilian.mayerhofer20
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Comment: C: Blast Output not in correct dir
... Jep, I tried full path, relative path or no path at all but everytime ( also with no specific path) it gets put into the genomes dir. ...
written 6 months ago by maximilian.mayerhofer20
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Comment: C: Blast Output not in correct dir
... even with the ".." it isnt outputting it correctly. ...
written 6 months ago by maximilian.mayerhofer20
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Comment: C: Blast Output not in correct dir
... problem is, even if I am in the script dir, the blast result are put into the genomes dir and not in the output dir. ...
written 6 months ago by maximilian.mayerhofer20
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Comment: C: Blast Output not in correct dir
... -out ../output/${F%.*}.xml but this says, go one folder above, into output and put it there? ...
written 6 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 6 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 6 months ago by maximilian.mayerhofer20 • updated 6 months ago by genomax57k
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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 7 months ago by maximilian.mayerhofer20

Latest awards to maximilian.mayerhofer

Scholar 6 months ago, created an answer that has been accepted. For A: Extracting specific IDs + sequence from multifasta
Scholar 7 months ago, created an answer that has been accepted. For A: Extracting specific IDs + sequence from multifasta
Scholar 8 months ago, created an answer that has been accepted. For A: Extracting specific IDs + sequence from multifasta

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