User: new15b

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new15b30
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n*****@my.fsu.edu

Posts by new15b

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Trimming ancient genomic DNA without existing alignment - leeHom or Adapterremov
... I found this paper about Adapterremoval where they claim version 2 is very suitable for ancient DNA: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4751634/ What is your opinion about this? I will look into BBMerge, thank you! ...
written 4 weeks ago by new15b30
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Trimming ancient genomic DNA without existing alignment - leeHom or Adapterremoval?
... Do any of you have experience with either leeHom or Adapterremoval? If you were working with a denovo assembly, would it make more sense to use one or the other for very ancient DNA? As someone very new to bioinformatics, I appreciate the thorough documentation for Adapterremoval, plus I don't have ...
genome sequencing written 4 weeks ago by new15b30
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Comment: C: Automating Trimmomatic for total Noobs
... I now have conda and Trimmomatic installed as a package - I tried to run the code: cat ids.txt | parallel 'trimmomatic PE {}R1*.f*q.gz {}R2*.f*q.gz {}pair_R1.fq.gz {}unpair_R1.fq.gz {}pair_R2.fq.gz {}unpair_R2.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLE ...
written 4 weeks ago by new15b30
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Comment: C: Automating Trimmomatic for total Noobs
... This business with Conda is in response to your suggestion, however. Without conda, I will not be able to download Trimmomatic as a python package and can't try any of your code. While this thread may look chaotic, it has a flow. You suggested I run Trimmomatic without jar, someone else hinted at ho ...
written 4 weeks ago by new15b30
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Comment: C: Automating Trimmomatic for total Noobs
... I downloaded conda to my directory and tried to install Trimmomatic. But I got this message: Solving environment: failed I was so happy that I got conda to install... and then this. EDIT: I got it to work with this: conda install -c bioconda trimmomatic ...
written 4 weeks ago by new15b30
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Comment: C: Automating Trimmomatic for total Noobs
... I don't have permissions to install anything to my server. All of those sudo commands online that I find do not work for me because they require a password. Leaving out sudo just gets it to ask me if I am root. I think I was utterly confused at how I got Trimmomatic to work as well. From what I can ...
written 4 weeks ago by new15b30
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Comment: C: Automating Trimmomatic for total Noobs
... Definitely not on my laptop - the files are too enormous and the computation too extreme for my poor computer. I only run things on the server. But I downloaded Anaconda2 to my laptop. ...
written 4 weeks ago by new15b30
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Comment: C: Automating Trimmomatic for total Noobs
... Okay stupid noob question: Will Conda download packages remotely to the school server even though it is located on my computer? Or do I have to move it to my school user directory? ...
written 4 weeks ago by new15b30
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Comment: C: Automating Trimmomatic for total Noobs
... Sure, why not? Anything that helps. ...
written 4 weeks ago by new15b30
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Comment: C: Automating Trimmomatic for total Noobs
... Yes, this issue of mine is improving a little with the Python course I am taking. Now, in retrospect, it seems obvious that I must be writing in shell language since I did not switch to Python in Terminal. At the time, not so clear. I am keeping this operation confined to one practice folder, so I ...
written 4 weeks ago by new15b30

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