Trimming Nextera adapter from scRNA paired reads with different length
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?
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