User: JV

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JV380
Reputation:
380
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Location:
Germany
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2 months, 2 weeks ago
Joined:
5 years, 2 months ago
Email:
j************@web.de

Posts by JV

<prev • 49 results • page 1 of 5 • next >
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Comment: C: Genome Annotation of a new bacterial strain
... How many contigs do you have? Did you check the overall assembly quality (e.g. with QUAST) and/or degree of potential contamination (you should always check ALL your assemblies with checkm)? I agree with jrj.healy that you should try prokka. It's the by far best automatic annotation program I have ...
written 11 months ago by JV380
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Comment: C: Low percentage of Illumina reads retained after trimming with Trimmomatic
... The fact that you retain only 20% of the reads when applying minlen after adapter-clipping fits perfectly with the "Adapter-Content" graph that shows that 80% of your reads carry the Universal adapter. My guess would be that probably your chloroplast DNA extraction/prep failed or is too contaminat ...
written 11 months ago by JV380
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Problem with Proteinortho.pl
... Since I can't find a specific "issues" page or contact adress for [Proteinortho][1], I'll try posting my problem here... I am currently using proteinortho v.5.16 for orhtolog detection. I ran it on a set of ~100 genomes and it worked fine. Then I realized that some of the input files were incomplet ...
software error orthologs homologs blast written 2.4 years ago by JV380 • updated 6 months ago by paulmjklemm0
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Comment: C: Orthology detection using proteinortho
... Can confirm that. "Bash on Ubuntu on Windows" is a relatively new feature introduced in Windows 10, and works great. [https://msdn.microsoft.com/de-de/commandline/wsl/install_guide][1] . Despite what many tutorials say, it DOES even support graphical user interfaces, you just have to install an X cl ...
written 2.4 years ago by JV380
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Answer: A: Merging of contigs files by minimus2
... I know this post is OLD. Just answering anyway, in case anybody else has problems with this. I got the same error message when testing minimus2 recently, and it turns out this was NOT because no overlaps would be detected (would have hoped for a more informative message on that, anyway). Turns out ...
written 2.5 years ago by JV380
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Comment: C: retrieving best hit in local blast output
... Well it sounds as if you only want to find the position of a certain set of genes within a genome of which you KNOW the queries are present (just don't know where exactly). So yeah, I think that is a case were you could safely rely on the first hit of each query filtered from the results-table. You ...
written 2.6 years ago by JV380
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Answer: A: retrieving best hit in local blast output
... Well basically, since the blast output is already sorted based on score and evalue, filtering in the way you have in mind would be LARGELY similar to using "-max_target_seqs 1" BUT not identical. The reason is that with the local alignment method used by BLAST, you often do not get one alignment per ...
written 2.6 years ago by JV380
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Comment: C: How to update Biopyhton?
... I tried updating pip several times. Still end up with the same old pip version. Seems to be the same issue as with the biopython update. Probably some conflict with the "System-python" V2.6 and my own python 2.7 (although can't remember having any issue with that before)? Anyway i ditched that comp ...
written 2.8 years ago by JV380
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Answer: A: How to update Biopyhton?
... OK never mind, I guess this has something to do with the fact that I have to maintain 2.6 as the "system"-python and have python 2.7 and python 3.5 installed in parallel. Never seemed to have in Issue with that before, but it seems the easiest way is to follow the general recommendation and only ...
written 2.8 years ago by JV380
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Comment: C: How to update Biopyhton?
... Well the shebangs of the *.py files in that folder seem to point either directly to this python executable or to "/usr/bin/env python" which in turn also points to this python executable ...
written 2.8 years ago by JV380

Latest awards to JV

Great Question 11 months ago, created a question with more than 5,000 views. For Downloading multiple species from ftp.ncbi.nih.gov using wget and wildcards
Appreciated 21 months ago, created a post with more than 5 votes. For A: Merging of contigs files by minimus2
Epic Question 21 months ago, created a question with more than 10,000 views. For Downloading multiple species from ftp.ncbi.nih.gov using wget and wildcards
Popular Question 21 months ago, created a question with more than 1,000 views. For How to use scripts with MEGAN5 in commandLineMode
Popular Question 21 months ago, created a question with more than 1,000 views. For specifying "GI mapping files" for MEGAN5 on command line interface
Popular Question 2.3 years ago, created a question with more than 1,000 views. For specifying "GI mapping files" for MEGAN5 on command line interface
Scholar 2.5 years ago, created an answer that has been accepted. For A: How to use scripts with MEGAN5 in commandLineMode
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: MEGAN5 help - no assigned reads
Supporter 2.7 years ago, voted at least 25 times.
Scholar 2.8 years ago, created an answer that has been accepted. For A: How to use scripts with MEGAN5 in commandLineMode
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Metavelvet issues. meta-velvetg.Graph2-stats.txt missing? Assembly not reproducable?
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Installation issues with hmmer2
Scholar 3.5 years ago, created an answer that has been accepted. For A: How to use scripts with MEGAN5 in commandLineMode
Great Question 4.1 years ago, created a question with more than 5,000 views. For Downloading multiple species from ftp.ncbi.nih.gov using wget and wildcards
Popular Question 4.1 years ago, created a question with more than 1,000 views. For assembly paired-end + single-reads together with idba_ud ?
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: MEGAN5 help - no assigned reads
Student 4.1 years ago, asked a question with at least 3 up-votes. For BLAST: Is there a difference between splitting queries and using more threads?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Metavelvet issues. meta-velvetg.Graph2-stats.txt missing? Assembly not reproducable?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Downloading multiple species from ftp.ncbi.nih.gov using wget and wildcards
Student 4.4 years ago, asked a question with at least 3 up-votes. For Downloading multiple species from ftp.ncbi.nih.gov using wget and wildcards
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Downloading multiple species from ftp.ncbi.nih.gov using wget and wildcards

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