Closed matbou85 closed 1 month ago
Follow up on this. Protocol doesn't work, you need to set up each parameter specifically.
But still, the clipping at 3p happens before adapter removal, so not useful. You could trim before using the pipeline and then skip trimming if you want to use correctly.
Should be fine now and addressed in #364 - please give dev
a try 👍🏻
Description of the bug
I am running
smRNAseq
on an HPC. My samples were prepared using the Nextflex library. The run was successful, please look at the code below, but the 4 bases from the 3 and 5' seem not to have been clipped.Command used and terminal output
Please see the first few lines of my original fastq file:
I have compared the trim results from the file found in miRDeep2 folder :
And the one found in output/mirna_quant/seqcluster/final:
Here are the results if I cut adapters and the 4 nucleotides in 3' and 5' using :
The log file from fastp seems to run this command :
I mainly wonder if four nucleotides are cut from the 3' and 5' end of the RNA as these should be removed according to the Nextflex pipeline. I have tested with an old version 1.1.0 and the 4 nucleotides from 3' and 5' were cut using the parameter --protocol 'nextflex'.