Critical appraisal of bioinformatics results

I think some biologists have a bit of a blind spot for bioinformatics when it comes to critical thinking. There may be a bit of a ‘well, the computer says this, therefore it is true’ attitude.

I think that any biologist who is interacting with bioinformatics/NGS results should take the following steps:

1. Take a complete reference genome from NCBI

2. Turn it into fastqs using e.g. pIRS

3. De novo assemble those fastqs. Oh, look at that, gives you a load of contigs!

4. Compare those contigs against the reference – start sweating.

5. Map your reads back to your contigs.

6. Call variants from that alignment – how does this strain have variants compared to itself? Have I created a new form of life, capable of mutating in silico? No, you haven’t.

7. Go and lie down in a dark room

 

Advertisements

3 thoughts on “Critical appraisal of bioinformatics results

  1. Pingback: Links 5/8/14 | Mike the Mad Biologist

  2. I realize your post was meant to be tongue-and-cheek but I’m still trying this anyways

    Question:

    What is the correct reference to grab from NCBI if were using pIRS?

    For example:

    1) ftp://ftp.ncbi.nih.gov/genomes/Arabidopsis_lyrata/
    File:NZ_ADBK00000000.scaffold.fna.tgz or File:NZ_ADBK00000000.contig.fna.tgz

    or

    2) ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Escherichia_coli_ABU_83972_uid161975/
    I assume the sequence data is segregated into directories for each *[not sure what?]*

    or, most of the reference genome folders look like this

    3) ftp://ftp.ncbi.nlm.nih.gov/genomes/Xenopus_Silurana_tropicalis/
    What would I choose in this case?

  3. I’m afraid I don’t have much experience with eukaryotic genomes. However, it looks like maybe the Xenopus genome is finished, while the arabidopsis genome is de novo assembled contigs from a short read experiment.

    In terms of the E. coli you point to, there is a plasmid and a chromosome in that directory. It is the .fna files you want (chromosome is the larger file). For the Xenopus, I imagine you want the CHR Un directory, and the .fa file within that. I guess the CHR Mt is the mitochondria? Please bear in mind that this is all complete guess work 🙂

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s