"Q1, Q2, Q3" Output of "stats" subcommand seems weird

[MapleHe]

Prerequisites

• make sure you're are using the latest version by seqkit version
• read the usage

Describe your issue

Platform: Linux
Data: raw 150bp fastq without trimming, number of reads: 42275372
Command: seqkit stats temp.fq -j 8 -a -T >>temp.tsv 2>>temp.log

seqkit Version v0.13.2 output:

Q1, Q2, Q3
150, 150, 150

seqkit Version v0.16.1, v2.3.0 output: (BTW, the version I downloaded is v2.3.1, but seqkit version shows v2.3.0)

Q1, Q2, Q3
75.0, 150.0, 75.0

When I downsample fastq to 1 read from the original fastq, using seqkit v0.13.2, output:

Q1, Q2, Q3
0, 150, 0

When I downsample fastq to 1 read from the original fastq, using seqkit v2.3.0, output:

Q1, Q2, Q3
75.0, 150.0, 75.0

Expected result:

Q1, Q2, Q3
150, 150, 150

As I understand, the Q1, Q2, Q3 should be the quartile of seq length, right ? Then v0.13.2 seems work as expected, for full dataset at least.

BTW, it could be better if there is an description/explatination of each column in the output in your document (maybe its my fault to omit it ?).

Thank you for your excellent tool.

[shenwei356]

Fixed it and added some docs:

• seqkit_darwin_amd64.tar.gz
• seqkit_windows_amd64.exe.tar.gz
• seqkit_linux_amd64.tar.gz

$ seqkit head -n 1 hairpin.fa | seqkit stats 
file  format  type  num_seqs  sum_len  min_len  avg_len  max_len
-     FASTA   RNA          1       99       99       99       99

simple statistics of FASTA/Q files

Columns:

  1.  file      input file, "-" for STDIN
  2.  format    FASTA or FASTQ
  3.  type      DNA, RNA, Protein or Unlimit
  4.  num_seqs  number of sequences
  5.  sum_len   number of bases or residues       , with gaps or spaces counted
  6.  min_len   minimal sequence length           , with gaps or spaces counted
  7.  avg_len   average sequence length           , with gaps or spaces counted
  8.  max_len   miximal sequence length           , with gaps or spaces counted
  9.  Q1        first quartile of sequence length , with gaps or spaces counted
  10. Q2        median of sequence length         , with gaps or spaces counted
  11. Q3        third quartile of sequence length , with gaps or spaces counted
  12. sum_gap   number of gaps
  13. N50       N50. https://en.wikipedia.org/wiki/N50,_L50,_and_related_statistics#N50
  14. Q20(%)    percentage of bases with the quality score greater than 20
  15. Q30(%)    percentage of bases with the quality score greater than 30
  16. GC(%)     percentage of GC content
  
Attentions:
  1. Sequence length metrics (sum_len, min_len, avg_len, max_len, Q1, Q2, Q3)
     count the number of gaps or spaces. You can remove them with "seqkit seq -g":
         seqkit seq -g input.fasta | seqkit stats

Tips:
  1. For lots of small files (especially on SDD), use big value of '-j' to
     parallelize counting.
  2. Extract one metric with csvtk (https://github.com/shenwei356/csvtk):
         seqkit stats -Ta input.fastq.gz | csvtk cut -t -f "Q30(%)" | csvtk del-header

The version I downloaded is v2.3.1, but seqkit version shows v2.3.0

Yes, I noticed that. Thanks for reporting.

[MapleHe]

Thank you for your quick answer and fix.