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import fastq format file

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import fastq format file

I have gene sequence file with the format is ".fastq".  How can I impout fastq file in to sas for data dealing? Thanks.


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‎10-03-2016 09:13 AM
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Re: import fastq format file

Posted in reply to Niugg2010

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Re: import fastq format file

Posted in reply to Niugg2010

It looks like it's a text file,so you can use standard text processing. That being said, it also looks like a complex file.

 

If you need assistance, its best to post a sample of the file, attach it as a .txt file or post in the message.

 

 

Frequent Contributor
Posts: 90

Re: import fastq format file

Thanks I will try. Actually I used Enterprise Guide to import, and then copy the code to sas to get data set.

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‎10-03-2016 09:13 AM
Valued Guide
Posts: 505

Re: import fastq format file

Posted in reply to Niugg2010

R is integrated with SAS IML so you should be able to use

 

http://svitsrv25.epfl.ch/R-doc/library/ShortRead/html/readFastq.html

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Re: import fastq format file

Posted in reply to rogerjdeangelis

Thanks.

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