User: new15b

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new15b30
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Posts by new15b

<prev • 22 results • page 1 of 3 • next >
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Comment: A: Setting paths for programs in a Json file when you have installed everything wit
... Thank you so much! I will try that as soon as I get in to the lab! I'll let you know if that works. I'm sorry these are such basic questions - most of us have no idea what we are doing (ZERO programming/computer science background) and are just winging it. Cheers!!! ...
written 20 days ago by new15b30
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Setting paths for programs in a Json file when you have installed everything with Conda.
... Hi! We are currently trying to navigate how to analyze Cut and Run data and are attempting to follow the pipeline protocol for the bioinformatical analysis available. This involves the manipulation of a Json file, which requires paths for all of the programs the pipeline needs to run. Unfortunately, ...
json conda written 23 days ago by new15b30
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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 9 months 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 9 months 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 9 months 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 9 months 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 9 months 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 9 months 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 9 months 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 9 months ago by new15b30

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Popular Question 9 months ago, created a question with more than 1,000 views. For Automating Trimmomatic for total Noobs

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