merge .fastq reads of different lengths and align

Question

[User6891]

Hi,

I have .fastq files from the same sample sequenced in two sequencing runs.

First run was on Illumina Hiseq and generated paired-end 2x100bp reads. Second run was on Miseq and generated paired-end 2x250bp reads.

Can I just merge the .fastq files of both runs (using cat), keeping off course R1 and R2 separate and then align with BWA? Or are the different read lengths going to pose a problem?

Answer 1

[Devon Ryan]

Different lengths aren't a problem. Note that it's unclear if these were sequenced from independent libraries or not. If they were, then you might want to keep them separate if you want to do variant calling, since there may be different biases between them.

Answer 2

[David Langenberger]

Of course, you can do that. Different read length do not influence the mapping algorithms. Actually, when clipping the adapter sequences, you end up with a lot reads having different read length.