samtools flags

I can never remember the order of the columns in samtools, so here they are

  1. QNAME: Query name of the read or the read pair
  2. FLAG: Bitwise flag (pairing, strand, mate strand, etc.)
  3. RNAME: Reference sequence name
  4. POS: 1-Based leftmost position of clipped alignment
  5. MAPQ: Mapping quality (Phred-scaled)
  6. CIGAR: Extended CIGAR string (operations: MIDNSHP)
  7. MRNM: Mate reference name (‘=’ if same as RNAME)
  8. MPOS: 1-based leftmost mate position
  9. INSIZE: Inferred insert size
  10. SEQ: Sequence on the same strand as the reference
  11. QUAL: Query quality (ASCII-33=Phred base quality)

There are lots more details in the samtools manual

You should also use the samtools flag explainer to understand column 2

Updating your ARC RMS research outputs

This is an Australian thing! If you are not from Australia, you probably don’t need to do this, but in case you do, here it is!

The ARC’s Research Management System has an outputs section that is, of course, mandatory, and is, equally of course, different from everyone else’s system.

I try and culture my references in Google Scholar, ORC ID, and my resume, and I don’t want to manually enter them into RMS, especially when a grant deadline is close. So here is one way to avoid that.

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minimap2 hints

Here are some tips and tricks for minimap2 that I keep forgetting!

–split-prefix

If you have a large (>4 GB) multisequence index file, there are two options.

The first is to increase the value of -I when you build the index (preferred) so that the whole index is kept in memory. Note: This must be done when you build the index, you can’t build the index and then change -I during runtime.

The second is to use --split-prefix with a string. For snakemake, there are two options:

  1. You can use "{sample}" as your prefix like so:
params:
    prfx = "{sample}"
...
shell:
    """
         minimap2 --split-prefix {params.prfx} ...
    """

2. You can use a random 6 character string like so:

import random, string

params:
        pfx = ''.join(random.choices(string.ascii_uppercase + string.digits, k=6)) 
...
shell:
    """
         minimap2 --split-prefix {params.prfx} ...
    """

The trick is here, things will probably break if your index file is small. If you see the errorr: [W::sam_hdr_create] Duplicated sequence it is probably because you have split a small index sequence, and the sequence IDs are being duplicated. Remove the --split-prefix option and you should be good.

Primer Trimming Challenge

In DNA sequencing, we add primers and adapters to the ends of sequences. These are short (typically <50bp) known sequences, that we use so we can identify different kinds of sequences. You can find out more about the adapters in this YouTube video.

This challenge is to write software to efficiently detect and remove the primers and adapters from a fastq format file.

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Global Distribution of Crassphage Map

How to make beautiful maps

Making maps is hard. Even though we’ve been making maps for hundreds of years, it is still hard. Making good looking maps is really hard. We published a map that is both beautiful and tells a story, and this is the story of how we made that map.

But a figure like this does not appear immediately, it takes work to get something to look this good, and needless to say it wasn’t me that made it look so great!

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Diversity, Equity, and Inclusion

Diversity, Equity, and Inclusion Statement

Diversity is a key element to the success of every organization and the tech community. Freedom of thought and the open exchange of ideas are key to an effective learning environment. That kind of exchange can happen only in an environment that recognizes the value of each person and fosters mutual respect. Rob Edwards and members of the Edwards Lab are committed to increasing and fostering a diverse community of colleagues.

Code of Conduct

We are dedicated to creating an inclusive environment for everyone, regardless of race, ethnicity, nationality, religion, skin color, sex, sexual orientation, gender identity, national origin, age, health (physical or mental), genetic information, parental status, marital status, political affiliation, veteran status, socioeconomic status or background, neuro(a)typicality, appearance, body size, computing experience, or clothing. Consider that calling attention to differences can feel alienating.

We do not tolerate harassment in any form towards any person. Harassment includes offensive verbal comments related to the classes above, sexual images in public spaces, deliberate intimidation, stalking, following, photography or audio/video recording against reasonable consent, sustained disruption of talks or other events, inappropriate physical contact, and unwelcome sexual attention (even without sexual contact). Harassment does not need to be recognized as unwanted or unwelcome by anyone other than the person being harassed. Be careful in the words that you choose. Remember that sexist, racist, and other exclusionary jokes can be offensive to those around you. Offensive jokes are not appropriate and will not be tolerated under any circumstances.

If you are being harassed, notice that someone else is being harassed, or have any other concerns, please immediately contact Dr. Rob Edwards

Equity

Inclusion and equity are not synonyms. Inclusion is just one part of equity, and to be equitable Rob and members of his lab strive to provide empowerment, agency, access, and respect.

  • Inclusion – Everyone is welcome in the lab. We all have strengths and weaknesses, and everyone contributes to every project.
  • Empowerment – As you work and study in the lab we want you to become more confident in your abilities and to grow as a person
  • Agency – we will enable you to make your own choices and to relish the successes that result from those choices
  • Access – we will be there to support you when you need us
  • Respect – we accept you for who you are

If you feel any of these are lacking, you should immediately talk to Rob or one of his supervisors.

Harassment Policy

Harassment of any kind is not acceptable behavior. We are committed to creating an environment in which every individual can work, study, and live without being harassed.

Harassment on the basis of race, ethnicity, nationality, religion, skin color, sex, sexual orientation, gender identity, national origin, age, health (physical or mental), genetic information, parental status, marital status, political affiliation, veteran status, socioeconomic status or background, neuro(a)typicality, appearance, body size, computing experience, or clothing. It includes harassment of an individual in terms of a stereotyped group characteristic, or because of that person’s identification with a particular group.

Sexual harassment may take many forms. Sexual assault and requests for sexual favors that affect educational or employment decisions constitute sexual harassment. However, sexual harassment may also consist of unwanted physical contact, requests for sexual favors, visual displays of degrading sexual images, sexually suggestive conduct, or offensive remarks of a sexual nature.

We are committed under this policy to stopping harassment and associated retaliatory behavior.

Anyone who feels harassed is encouraged to seek assistance from Rob or his supervisors.

About

This Code of Conduct was adapted from the Make School Code of Conduct, which in turn was adapted from Hack Code of Conduct which was inspired by the Conference Code of Conduct. The harassment policy has been adapted from MIT’s Harassment Policy.

Licensed under Creative Commons 4.0 (Attribution, Share Alike).