trim galore putfiles
1 answer
val*.fq files are the output files after validation as mentioned in the manual:
option ‘--paired’ which runs a paired-end validation on both trimmed _1 and _2 FastQ files once the trimming has completed. This step removes entire read pairs if at least one of the two sequences became shorter than a certain threshold.
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I have the same question! I ran trim_galore as follows:
trim_galore --paired -stringency 5 -length 50 -q 20 -o ./MYFASTQ_1.fastq MYFASTQ_2.fastq
...and it output 6 files:
MYFASTQ_1_trimmed.fq (19 Gb)
MYFASTQ_2_trimmed.fq (19 Gb)
MYFASTQ_1.fastq_trimming_report.txt
MYFASTQ_2.fastq_trimming_report.txt
MYFASTQ_1_val_1.fq (6.2 Gb)
MYFASTQ_2_val_2.fq (6.2 Gb)
What are the val files?