(alevin) Specifying --read-geometry in paired-end samples

[yyoshiaki]

Hello,
I would like to use alevin for quantification of 10x 5' PE. 10x 5' PE contains cDNA in read1 as well as read2. Could you tell me how to specify the --read-geometry to use both read1 and read2 for quantification.

The configuration of the library is as follows
read1 BC16bp-UMI10bp-TSO13bp-cDNA5'
read2 cDNA3'

I tried the following library options, but I got "Total 0.00 UMI after deduplicating.
-l ISF --bc-geometry 1[1-16] --umi-geometry 1[17-26] --read-geometry "1[40-end]2[1-end]"

I also tried "1[40-end] 2[1-end]" and "1[40-end],2[1-end]" by changing the delimiter, but they were not quantified in the same way. On the other hand, "1[40-end]" and "2[1-end]" were quantified well.

Best,
Yoshi