Hi, I have an fundamental question...
as you know, paired-end fastq files(ex. 'asdf.for.fastq' and 'asdf.rev.fastq') can be aligned to 'asdf.sam'
As I know, aligner program aligns each forward read and reverse read of paired-end read(which have same seq ID) seperately.
So, we can see that forward read can be aligned but reverse read cannot.
however, I think that forward and reverse read must be merged before aligned and the merged one read should be aligned to reference as a 1 set.
please give me any advice.
Sorry for NEWBIE question.
as you know, paired-end fastq files(ex. 'asdf.for.fastq' and 'asdf.rev.fastq') can be aligned to 'asdf.sam'
As I know, aligner program aligns each forward read and reverse read of paired-end read(which have same seq ID) seperately.
So, we can see that forward read can be aligned but reverse read cannot.
however, I think that forward and reverse read must be merged before aligned and the merged one read should be aligned to reference as a 1 set.
please give me any advice.
Sorry for NEWBIE question.
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