fq-count¶
Count the number of reads in a FASTQ and calculate additional metrics.
Counts lines in a FASTQ
Usage:
fq-count [options] [fastq ...]
Arguments:
[fastq ...] Input FASTQ
Options:
-t, --header Output the header
-b, --basename Add basename column
-a, --absolute Add column for absolute path
-h, --help Show this help
Example¶
sc fq-count --header -b *.fq
| reads | gc_content | gc_bases | n_bases | bases | basename |
|---|---|---|---|---|---|
| 8 | 0.53125 | 17 | 0 | 32 | dup.fq |
| 8 | 0.53125 | 17 | 0 | 32 | dup.fq.gz |
| 1 | 0.35 | 21 | 0 | 60 | illumina_1.fq |
| 1 | 0.35 | 21 | 0 | 60 | illumina_2.fq |
| 1 | 1 | 101 | 0 | 101 | illumina_2000_2500.fq |
| 6 | 0.35 | 126 | 0 | 360 | illumina_3.fq |
| 1 | 1 | 101 | 0 | 101 | illumina_3000_4000.fq |
| 1 | 0.35 | 21 | 0 | 60 | illumina_4.fq |
| 1 | 0.35 | 21 | 0 | 60 | illumina_6.fq |
| 1 | 0.35 | 21 | 0 | 60 | illumina_7.fq |
| 2 | 0.333333 | 14 | 0 | 42 | illumina_8.fq |
| 1 | 0.35 | 21 | 0 | 60 | illumina_hiseq_x.fq |
| 4 | 0.5 | 8 | 0 | 16 | nodup.fq |
| 9 | 0 | 0 | 0 | 9 | novaseq.fq |
| 2 | 0.430556 | 62 | 0 | 144 | sra.fq |