trim_galore output: val_1 and val_2 files??

Question

[radlinsky]

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?

Answer 1

[h.fushimi.x689]

As I understand, Trim galore! trims each read separately. These results are _trimmed.fq files. So some spots may have only one read after trimming because the other read becomes too short. But some downstream analyses require exactly same spots data for both reads. So the software removes single read spots. This results are val_1/2.fq files.

Answer 2

[st.ph.n]

From release notes:

07-02-13: Version 0.2.6 released

Fixes some bugs which would not gzip or run FastQC correctly when the option '-o' had been specified
When '--fastqc' is specified in paired-end mode the intermediate files '_trimmed.fq' are no longer analysed (only files '_val_1' and '_val_2')

[GenoMax]

That does not answer the question asked. OP is not using --fastqc option either. val files may be properly paired reads remaining after trimming but I am not 100% sure.