Trimming Nextera adapter from scRNA paired reads with different length

Question

[almogangel]

Hi everyone,

I have two FASTQ files (R1 and R2) which R1 is 50bp (cDNA) and R2 is 17bp (BC+UMI). I would like to trim the Nextra adapters with Trim Galore and to keep only reads that are >35bp in R1 and the full length (17bp) in R2.

I tried using:

trim_galore --nextera --paired --length 35 --paired --fastqc -o nextera_trimmed_fastq --cores 8 *.fastq.gz

But all reads have been removed since R1 is shorter than 35bp.

Is there a way to specify the "length" parameter for R1 and R2 separately?

Thanks!