Monthly Archives: June 2021

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.

Continue reading