Hi all,
I have paired end RNA seq data in bcl format that I want to convert to fastq format (using CASAVA 1.7/1.8).
I know that CASAVA doesn't do paired-end alignment for RNA data, so the plan is to align using a third-party tool such as BowTie.
The question is whether the data will be preserved in paired-end format after the conversion by default? If not, what steps are necessary to preserve the paired-end data?
[I am not sure if it makes any difference, but just as a note, the data will be demultiplexed as a separate step after FASTQ conversion because I am not able to do the bcl conversion and demultiplexing in one step (due to compatibility issues).]
Thanks!
I have paired end RNA seq data in bcl format that I want to convert to fastq format (using CASAVA 1.7/1.8).
I know that CASAVA doesn't do paired-end alignment for RNA data, so the plan is to align using a third-party tool such as BowTie.
The question is whether the data will be preserved in paired-end format after the conversion by default? If not, what steps are necessary to preserve the paired-end data?
[I am not sure if it makes any difference, but just as a note, the data will be demultiplexed as a separate step after FASTQ conversion because I am not able to do the bcl conversion and demultiplexing in one step (due to compatibility issues).]
Thanks!
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