Question: Cutadapt and FastQC
gravatar for bioinformaticsfilesdrive
2.8 years ago by

Hi all,

I currently am using cutadapt on windows- thanks @emmaggie on Cutadapt On Windows for the help!

I was able to remove the adapter sequence of interest after one round of cutadapt, as seen in these pictures.

However, I am now left with a huge amount of blank reads- how do I get rid of them? Also, I seem to have had other overrepresented sequences taken away as well. Based on the images, should I be happy with that- were they probably adapters? Should I trim the other sequences away?

Thanks for any and all help!



fastqc rna-seq cutadapt ngs • 1.5k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by bioinformaticsfilesdrive0

Instead of trying to do this locally, you'd be better off uploading the files to and using trimmomatic or "Trim Galore!" there. In general, windows isn't well supported by bioinformatics tools.

ADD REPLYlink written 2.8 years ago by Devon Ryan94k

Sorry just seeing this now. I've been told that tool wont work with my data since my data is in SOLiD colorspace and I have read that converting to basespace before alignment isn't good. Please let me know if the tool will work or not- all of the data is on galaxy already. Do you know how to remove the blank reads cutadapt makes?

ADD REPLYlink written 2.8 years ago by bioinformaticsfilesdrive0

since my data is in SOLiD colorspace

You should have mentioned important information such as this in your initial question. Please try to be as informative as possible.

ADD REPLYlink written 2.8 years ago by WouterDeCoster43k

Apologies- what do you recommend I do from here with the blank reads?

ADD REPLYlink written 2.7 years ago by bioinformaticsfilesdrive0
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