trim galore putfiles
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6.2 years ago
blur ▴ 260

Hi,

I am running trim galore, but didn't speficy an outfile name - are the trimmed files the once marked val1.fq and val.fq?

Thanks

trim galore • 3.1k views
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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?

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Entering edit mode
5.5 years ago
Sej Modha 5.2k

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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