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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
The text was updated successfully, but these errors were encountered:
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
The text was updated successfully, but these errors were encountered: