Issues with adapter trimming when there are no adapters?
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Entering edit mode
10 months ago
dare_devil ★ 1.5k

When I run fastqc on my sample, it did not identify any adaptor sequence in the sample but there were some low quality reads in the sample. Then I used trim galore to remove the low quality reads using following command:

trim_galore --illumina --gzip --fastqc -o trimmed -j 4 --paired $Read1 $Read2

but in this when I checked the log file I was able to see some adaptors detected in the file. How is this possible? Are there any way to trim only low quality reads?

=== Summary ===

Total reads processed:             115,217,093
Reads with adapters:                40,928,868 (35.5%)
Reads written (passing filters):   115,217,093 (100.0%)

Total basepairs processed: 11,521,709,300 bp
Quality-trimmed:             199,850,659 bp (1.7%)
Total written (filtered):  11,118,622,037 bp (96.5%)
fastqc cutadapt adapters illumina trimgalore • 431 views
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3
Entering edit mode
10 months ago
GenoMax 107k

Are there any way to trim only low quality reads?

FastQC does not look at every read when it does QC. It sub-samples data. This is fine for QC purposes and done in view of time/memory considerations. Where as a program like trim_galore is doing an operation it looks at every read in your dataset.

If you want to leave reads with adaptors in (which BTW are likely going to carry a lower quality, so you are going to remove some of those) and trim only based on Q scores then you could try bbduk.sh from BBTools. trim_galore likely could be used in a similar mode. You may want to check into command line options.

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