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Old 01-14-2013, 05:25 PM   #1
xfh
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Default how could I know whether the adaptor has been trimed

Dear all,

Here I have a question about the data analysis about NGS. I download the pair-end fastq files about WGBS on EBI, but I don't know what is the adaptor that used and I want to ask how can I know whether it has been removed?

Thanks all for you answers.
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Old 01-15-2013, 04:11 AM   #2
GenoMax
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You can always try contacting the original submitter of the sequence to get additional information.

You will need to have some idea about what kind of sequencing results these are in order to effectively use a tool such as "trimmomatic". http://www.usadellab.org/cms/index.php?page=trimmomatic

You can look at the thread below to obtain the sequences of the illumina adapters.

http://seqanswers.com/forums/showthr...adapter&page=2

That said most of the publicly released data should have the adapters trimmed (except few reads where there may be adapter dimers etc, in case the sequences are not QC'ed).
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Old 01-15-2013, 05:17 AM   #3
rahularjun86
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Hi,
You can look here: http://intron.ccam.uchc.edu/groups/t...Sequences.html
unix grep command can be used for rough idea of adapters and primers in your sequences. Here are the tools to trim the adapters: http://bioscholar.com/genomics/tools...quencing-data/

Hope this will help.

Regards,
Rahul
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Old 01-15-2013, 05:22 AM   #4
twaddlac
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Clustering the reads may shed light on what the adaptor sequence is. You could cut n bases from the 5' end of the reads and cluster them using cd-hit-est (http://weizhong-lab.ucsd.edu/cd-hit/) and based on how many reads cluster into a specific sequence you could identify the common sequence which would presumably be the adaptor.

Hope this helps, good luck!
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Old 01-15-2013, 03:57 PM   #5
xfh
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thank all for your reply, i will have a try.

Last edited by xfh; 01-15-2013 at 05:28 PM.
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Old 01-15-2013, 05:10 PM   #6
BAMseek
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You might try FastQC and look at over-represented sequences to see if there are adapters.

seqdiverse might also shed some light on that (I wrote it so feel free to ask me questions or complain).

Justin

Last edited by BAMseek; 01-15-2013 at 05:12 PM. Reason: changed url
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Old 01-15-2013, 05:26 PM   #7
xfh
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Great, I will use seqdiverse to make a try, thank you very much.

Quote:
Originally Posted by xfh View Post
thank you for your reply, i will have a try.
Quote:
Originally Posted by BAMseek View Post
You might try FastQC and look at over-represented sequences to see if there are adapters.

seqdiverse might also shed some light on that (I wrote it so feel free to ask me questions or complain).

Justin
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