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Question about htseq-count for SS3 and VASA-seq #1

Closed biobenkj closed 1 week ago

biobenkj commented 1 month ago

Hello! Thank you so much for including all the code for reproducing analysis! I wanted to ask about treating the strandedness for Smart-seq3 and VASA-seq (plate). Were these treated as unstranded for gene detection counting? I assume so with the -s no but wanted to ask. Thanks!

biobenkj commented 2 weeks ago

just bumping this question up

biobenkj commented 1 week ago

another bump. thanks!

ychniu commented 1 week ago

Hello! Thank you so much for including all the code for reproducing analysis! I wanted to ask about treating the strandedness for Smart-seq3 and VASA-seq (plate). Were these treated as unstranded for gene detection counting? I assume so with the -s no but wanted to ask. Thanks!

Hi Ben,

In order to achieve equal-footing comparison, we also treated them as unstranded for gene detection counting.

Yichi

biobenkj commented 1 week ago

Thank you