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Question: how to find adaptor sequences
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gravatar for ajmaninisha
3.7 years ago by
ajmaninisha • 30
Canada
ajmaninisha • 30 wrote:

Hi 

 

How can i find the adaptor sequence in my reads.
forum adaptor sequences • 2.0k views
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modified 3.7 years ago • written 3.7 years ago by ajmaninisha • 30
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gravatar for Jennifer Hillman Jackson
3.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Do you know what the sequences are? If so, the tool "NGS: QC and manipulation -> Clip adapter sequences" is a good choice.

If you do not know what these are, try contacting whomever did the sequencing. Or you can try using "FastQC" to identify them.

Best, Jen, Galaxy team
ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k

Thankyou I know about the sequences but they have annotated file in asn format so I don't know how it's going to work Also there is an option to customize Tophat like mean square distance inner distance etc.

Kindly advise how to use it and calculate it. Thankyou

Regards

Nisha

ADD REPLY • link written 3.7 years ago by ajmaninisha • 30
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gravatar for ajmaninisha
3.7 years ago by
ajmaninisha • 30
Canada
ajmaninisha • 30 wrote:

I used FASTQC and from its results checked the overrepresented sequences and used Clip. Now, the problem i am facing is i have a reference genome but its annnotation file is in asn format, how can i use this in galaxy.

 

Also, please advise in customizing the parameter for Tophat2 likle how to calculate inner mean distance etc
ADD COMMENT • link written 3.7 years ago by ajmaninisha • 30
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