how to align paired and unpaired fastq files of a sample using STAR?

Question

[milad eidi]

Hi all I'm new to using STAR aligner. I have PE sequencing fastq files which have forward and reverse pairs and forward and reverse unpairs reads (4 files). In the manual of this tool, it seems they don't consider unpairs reads of a sample. Could anybody help me?

Answer 1

[seidel]

Do you have 4 files as a result of read trimming? You could align the paired-end data as usual, and align it in paired-end mode. The other files you could treat as single end data, and align them accordingly. If you're measuring gene expression, you'd simply have to combine counts from different files afterwards.

[milad eidi]

yes, i got them from trimming. thanks

Answer 2

[swbarnes2]

Align them separately, then merge the bams. If the unpaired files are only a fraction of the size of the paired ones, you might just omit them.