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mscook / SeqFindR

A tool to easily create informative genomic feature plots
http://mscook.github.io/SeqFindR/
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General clarification requests to be integrated in the tutorial #31

Closed areejalsheikh closed 10 years ago

areejalsheikh commented 10 years ago

If you could please explicitly mention the following in the tutorial, it would be great:

  1. The assemblies and consensus directories need to have the same number of files.
  2. Preferably, no other files other than the assemblies and consensus must be present in the the respective folders (e.g. README)
  3. Make sure that the number of strains mentioned in the order index file match the number of assemblies and consensus you are parsing
  4. If you must use complete genomes, simply add their fasta file in the assemblies and the consensus directories. Note that you must rename them to follow the same naming scheme (including the file extension) for the rest of the files in each directory (e.g. for a strain called: XXX_consensus.fa, the complete genome must be called: YYY_consensus.fa - cannot be .fasta)
  5. If you use nesoni, by default it creates consensus.fa files (I think). In this case you do NOT have to follow the "How to generate mapping consensus data" tutorial.

*Speaking of the mapping consensus section:"

First: please note that the tutorial for mapping consensus generation in the page (https://github.com/mscook/SeqFindR) is incomplete, and rather confusing, compared to the one here (https://github.com/mscook/SeqFindr_nesoni). Perhaps you can explicitly say to follow the more detailed one (SeqFindr_nesoni).

  1. Please explicitly say that one must first download the package, in order to be able to use the commands listed in the tutorial
  2. Please emphasise that the reads.dat is pointing at the trimmed reads generated after QC, usually. I only figured it out when I saw the extension ".compression"! I thought that I will have to use reads.dat pointing at mapping reads, for some reason.
  3. Perhaps mention that if one runs nesoni, it usually automatically generates "consensus.fa" output, and therefore, this tutorial is unneeded.

Sorry for the long "issue", I just thought that the clearer it is, even if it's rather obvious, the better the tutorial would be :)

Thanks, Areej