Question: Cutadapt and FastQC
0
gravatar for bioinformaticsfilesdrive
22 months 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.

https://ibb.co/jcGGkF

https://ibb.co/nBnvea

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!

Sincerely,

bioinformaticsfiledrive

fastqc rna-seq cutadapt ngs • 1.0k views
ADD COMMENTlink modified 22 months ago • written 22 months ago by bioinformaticsfilesdrive0
1

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

ADD REPLYlink written 22 months ago by Devon Ryan90k

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 22 months 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 22 months ago by WouterDeCoster38k

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

ADD REPLYlink written 22 months ago by bioinformaticsfilesdrive0
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