How to ignore bases with bcl2fastq2 --use-bases-mask

Question

[Can Holyavkin]

Hello,

How can I ignore the first bases of index reads with bcl2fastq2 --use-bases-mask option?

The index read has 8 cycles, but I want to use only "last 7" of them. illumina bcl2fastq manual only mention about ignoring the last reads, not ignoring the first reads.

I tried the following option but it didn't work.

--use-bases-mask y151,nI7

Answer 1

[Dan D]

You were very close:

--use-bases-mask y151n,I7

[Can Holyavkin]

:D Oh! Thank you.

[Yizhao]

Hi, Dan. Now I have the same problem with Can. But I want to ignore the last base of index. How to do that? Could you give me more explanation on the parameter --use-bases-mask? what is meaning of y151n,I7? I've checked the manual illumina supported, but I cannot make it clear. Thanks.

[Yizhao]

I have got it. But still thx the post. best:)

BTW, the example in the manual of bcl2fast, not bcl2fastq2, is very helpful.