Question: How to ignore bases with bcl2fastq2 --use-bases-mask
2
gravatar for Can Holyavkin
4.2 years ago by
Can Holyavkin240
Turkey
Can Holyavkin240 wrote:

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 worked. 

--use-bases-mask y151,nI7
masking bcl2fastq illumina • 4.0k views
ADD COMMENTlink modified 4.2 years ago by Dan D6.8k • written 4.2 years ago by Can Holyavkin240
4
gravatar for Dan D
4.2 years ago by
Dan D6.8k
Tennessee
Dan D6.8k wrote:

You were very close:

--use-bases-mask y151n,I7

ADD COMMENTlink written 4.2 years ago by Dan D6.8k

:D Oh! Thank you. 

ADD REPLYlink written 4.2 years ago by Can Holyavkin240

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 REPLYlink written 4.2 years ago by Yizhao10

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

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

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Yizhao10
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