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%)
1 answer
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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Kevin
Why is Kevin tagged in this post? Does this post have anything to do with a tool he developed?
I have seen him in many post answering the questions very effectively.
There also some people who always come and
itchesthenewbiein the forum wasting time on the both ends. This might be the reason that I did not tag youIf you'd like to get an answer from Kevin specifically, I'm sure he has a freelancing hourly charge. It is bad etiquette to tag individual users on a professional forum.
_r_ram Hi, you asked me the reason for tagging. Now you have removed the entire comments from here.
Why did you do that?This forum is not only for paid persons. If people are willing to help, let them help. Moreover, I have seen you in many post itching the newbie without a proper reason. Why don't you mention rules and regulations of the forum to the newbie if he/she is not posting the comments the right way.The comments were not relevant to the topic at hand. I wanted to avoid the exact thing you're doing right now, which is ad hominem attacks.
I'm here to help people with bioinformatics and keep the forum professional. Learning to be professional is up to the individual though. I don't understand what you mean by "itching the newbie".
Once again, you are welcome to discuss this offline on our slack group - the forum is not the place for this discussion.
Hi dare_devil,
Please be more professional. Tagging someone is rude. If a moderator explains to you the etiquette of using a Q&A forum then there is no need to get defensive and attack the moderator instead. Such behavior will not be tolerated.
Best,
Wouter
my mistakesorry for the rude comments @ _r_am @WouterDeCoster.Can you remove all the unwanted comments from the section ?