How to normalise read depth in scRNA-seq data, with usegalaxy

Question

[ikokkinopoulos]

Hello all,

I have a number of C1 fluidigm scRNA-seq data (paired-ended) using Smart-Seq2, but with different sequencing depths. Is it possible to normalise for sequencing depths in usegalaxy after using STAR to map them on the mouse genome?

Also, can one also compare single-end and paired-end data after mapping them?

Cheers,

Y

[ATpoint]

Please ask at the Galaxy forum: https://galaxyproject.org/support/