Question: Interpreting trim_galore report
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gravatar for vaslanzadeh
23 months ago by
vaslanzadeh0 wrote:

Hello, I have a single-end small RNA-seq data and to filter out adaptors and trim low quality bases I used Trim Galore. I am new to RNAseq data analysis and have a question about trim_galore report. I understand some part of the report except "Total written (filtered):". What does it mean? Is it number of the bases with good quality which passed the filtering(18.6%)? If so, does it mean 82.4% of the bases had low quality and were trimmed off!? At the end, trim_galore removes 75.7% of the reads. Thanks

This is cutadapt 1.13+1.g6b2366d with Python 2.7.10 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG BacRNA_sequence.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ...

Total reads processed: 3,876,983

Reads with adapters: 3,668,488 (94.6%)

Reads written (passing filters): 3,876,983 (100.0%)

Total basepairs processed: 139,571,388 bp

Quality-trimmed: 2,391,351 bp (1.7%)

Total written (filtered): 26,018,981 bp (18.6%)

. . .

3876983 sequences processed in total

Sequences removed because they became shorter than the length cutoff of 16 bp: 2933098 (75.7%)

rna-seq • 1.1k views
ADD COMMENTlink written 23 months ago by vaslanzadeh0

Is it number of the bases with good quality which passed the filtering (18.6%)? If so, does it mean 82.4% of the bases had low quality and were trimmed off!?

Yes, you are correct in your interpretation.

ADD REPLYlink written 23 months ago by h.mon26k
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