run simpleaf with a different umi length (here 9) | add-chemistry successfully

[robertzeibich]

I tried to process my FASTQ files with UMI length 9 instead of 10 (10xv2) or 12 (10xv3).

R1: 25 --> 16 barcode and 9 UMI
R2: 50

To do so, I added a chemistry. However, I faced the following error message:

simpleaf add-chemistry --name honey --geometry 1{b[16]u[9]x:}2{r:}
2024-11-08T09:40:10.563033Z INFO simpleaf::simpleaf_commands::chemistry: inserting chemistry honey with geometry 1{b[16]u[9]x:}2{r:}
Error: Cannot automatically obtain an unfiltered permit list for non-Chromium chemistry : 1{b[16]u[9]x:}2{r:}

Instead of using the --unfiltered-pl , I should have used --knee.

While this resolves the add-chemistry error, I still could not align my FASTQ files.

Error: piscem mapping failed with exit status ExitStatus(unix_wait_status(134))

Instead of using a piscem-based index, I should have created an salmon-based index, which can be created by using the option --no-piscem in the simpleaf index command.