Aligning multiple runs using STARSolo

Question

[AB]

Hi all,

This question might be basic but it has gotten me confused. I download single cell RNASeq data for a sample from GEO using SRAtoolkit. As you can see here, this particular sample has 4 runs. So when running STARSolo using the following command, would it be right to comma-separate the runs ?

STAR --genomeDir ~/ngs/mm10_STARSolo --readFilesIn run1_R2,run2_R2,run3_R2 run1_R1,run2_R1,run3_R1  [...other parameters...]

Thanks

Answer 1

[ATpoint]

Please read the manual section 3.2: https://raw.githubusercontent.com/alexdobin/STAR/master/doc/STARmanual.pdf

Yes, comma separates multiple files.

[AB]

Thank you very much. I was looking at the STARSolo documentation and it mentions so for multiple lanes.