Question: editing lane number in number of fastq files
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gravatar for rob.costa1234
4.4 years ago by
rob.costa1234250
United States
rob.costa1234250 wrote:

I want to edit lane numbers in fastq files as core ran into different lanes, base space will not recognize different lane numbers. What may be the best strategy.

Thanks .

fastq • 1.4k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by rob.costa1234250

I assume you are referring to changing the numbers inside the file (and not just the file name)? That may not be advisable. There is a small chance that there will be a conflict between tile:X:Y coordinates for reads from two different lanes.
Why is base space not recognizing lane numbers (as long as they are in standard Illumina format).

ADD REPLYlink written 4.4 years ago by genomax91k

You are right I want to change the FAstq file header s which are coming from different lanes. Base space is not recognizing cat different fastq files coming from different lanes so it was suggested by illumina to change the lane number to make them consistent otherwise basespace throws error that headers are not compatible.

ADD REPLYlink written 4.4 years ago by rob.costa1234250

You could do the following (select the fastq header from your file up to lane # (I am changing lane # from 2 to 8 in example below

sed 's/@EAS139:136:FC706VJ:2/@EAS139:136:FC706VJ:8/g' your_orig.fastq > changed.fastq

You may get an error about duplicate ID's in case the changed ID exists.

ADD REPLYlink modified 4.4 years ago • written 4.4 years ago by genomax91k
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