bcl to fastq convert for only two lane

Question

[BioRyder]

Hello,

I want to convert bcl to fastq for 4 & 6 lane only by using bcl2fastq. I have tried to use --tiles s_[4,6], but it returns error. Please someone can tell me how to use --tiles option extract fast only for 4 and 6 lane.

Answer 1

[Pierre Lindenbaum]

--tiles option takes a comma-separated list of regular expressions to match against the expected "s_<lane>_<tile>" pattern, where <lane> is the lane number (1-8) and <tile> is the 4 digit tile number (left-padded with 0s).

so you need something like:

--tiles s_[46]_[0-9][0-9][0-9][0-9]

[BioRyder]

It worked. I used --tiles s_[46].Thank you so much