Question

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

2

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9.5 years ago

Can Holyavkin ▴ 250

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

bcl2fastq illumina masking • 6.9k views

ADD COMMENT • link updated 22 months ago by Ram 44k • written 9.5 years ago by Can Holyavkin ▴ 250

Ram · Accepted Answer · 2015-06-05

4

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9.5 years ago

Dan D 7.4k

You were very close:

--use-bases-mask y151n,I7

ADD COMMENT • link 9.5 years ago by Dan D 7.4k

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:D Oh! Thank you.

ADD REPLY • link updated 22 months ago by Ram 44k • written 9.5 years ago by Can Holyavkin ▴ 250

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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.

ADD REPLY • link updated 5.1 years ago by Ram 44k • written 9.4 years ago by Yizhao ▴ 10

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

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

ADD REPLY • link 9.4 years ago by Yizhao ▴ 10