Hi!!
I am trying to run kneadData on bash but I got the following output files after processing my raw files (3158_R1.fastq.gz and 3158_R2.fastq.gz) ) on Paired-End-Run mode:
Output files obtained:
-reformatted_identifiers5J47Ei_decompressed_1J7Skd_SRR19109032_pass_2 SRR19109032_pass_1_kneaddata.log
-reformatted_identifiersqmnaMs_decompressed_7QYa6i_SRR19109032_pass_1
-SRR19109032_pass_1_kneaddata.log
I would like to clarify that my data is raw and not have been trimmed, so the problem comes because I didn’t trim before using kneadData?
Script:
kneaddata --input /mnt/Micro/villafandata/SRR191090$line_pass_1.fastq.gz --input /mnt/Micro/villafandata/SRR191090$line_pass_2.fastq.gz --reference-db /mnt/BUNDLE_38/GRCh38_noalt_as --output /mnt/Micro/kneaddata_controles/$line --bypass-trim
Thanks for read me!!
Best
Isra