Custom Adapter Sequence in Kneaddata

Infrastructure and utilities KneadData
1

Hello, I would like to use kneaddata with a custom adapter sequence, rather than the ones pre-installed (ie. TruSeq2, TruSeq3, NexteraPE). I have the sequence set up as a .fa file. But I can’t figure out how to get kneaddata to use my adapter FASTA file.

Additionally, I tried to use trimmomatic to trim the adapters then pass the sequence off to kneaddata with the flag --bypass-trim since I already trimmed the adapters:

kneaddata --input1 /path/to/trimmed/sequence/test_001_S77_L004__trimmed_1P.fastq.gz \
    --input2 /path/to/trimmed/sequence/test_001_S77_L004__trimmed_2P.fastq.gz \
    -db /path/to/reference_db/mouse \
    --run-trim-repetitive \
    --run-fastqc-start \
    --run-fastqc-end \
    --bypass-trim \
    --threads 32 \
    --output /writeable/path/kneaddata/

but I ended up with an error: ERROR: Unable to write file: /writeable/path/kneaddata/reformatted_identifiers4yt3gtxj_decompressed_ijjeqjgd_test_001_S77_L004__trimmed_1P

Any help is appreciated!

I am using
[kneaddata v0.12.2]

2

Update: So I figured out what was causing the error. Turns out the Kneaddata requires the input files to have the format of filename.R1.fastq.gz and filename.R2.fastq.gz despite using the --input1 and --input2 flags. Hopefully if anyone comes across this issue, this helps!

But I still am not sure how to specify custom adapter sequences in kneaddata or if that’s even possible.