I'm having some trouble with my output files after I use trim galore. I think I might have found the issue but I'm curious if anyone has had a similar problem. The command I give trim galore specifies paired end mode but for some reason cut adapt is trimming in single end mode. Anyone know if this is a bug or am I thinking about this wrong?
Below is my trim_galore report . I highlighted in bold my what I mean...
SUMMARISING RUN PARAMETERS
Input filename: Regeneration_ATAC_1hpa-1_R1.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.1
Cutadapt version: 1.10
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; user defined)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
All sequences will be trimmed by 1 bp on their 3' end to avoid problems with invalid paired-end alignments with Bowtie 1
Running FastQC on the data once trimming has completed
Output file will be GZIP compressed
This is cutadapt 1.10 with Python 2.7.11
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA Regeneration_ATAC_1hpa-1_R1.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1463.06 s (25 us/read; 2.45 M reads/minute).