How does this work on Paired-end(1 samle - 1.fq.gz and 2.fq.gz)

[kuangzhuoran]

Hi ! Thank you very much for developing such a convenient tool.

run "atlas init --db-dir databases /PATH/", It told me "Found 24 samples under /PATH/" actually I have 12 samples(24 fq.gz, because they are Paired-end, 12 x 2 = 24)

When I dry run, I see "B3-2_raw_se.fastq.gz" and "verifypaired=f" So It seems that its default setting does not support Paired-end,

My current idea is : cat A-1.fq.gz A-2.fq.gz > A-fq.gz, so it may work properly on sample A, And I just need to do this for all 12 samples

Best kzr

[kuangzhuoran]

im so sry, I download test data and I know why Just name it in this format： sample_R1.fq.gz sample_R2.fq.gz