How to convert .cel to .fastq for miRNA analysis?

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5.5 years ago

nkabo ▴ 80

I would like to do miRNA analysis for a dataset that I have found via an article. The pipeline I have in order to analyze the miR data requires the data file to be a .fastq file. However, the dataset I received is composed of .cel files. Is it possible to convert .cel datafiles to .fastq? Thanks

miRNA analysis RNA sequencing next-gen • 2.6k views

ADD COMMENT • link 5.5 years ago by nkabo ▴ 80

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.cel files are affymetrix array file and .fastq are from sequencing as I understand. Look at the methodologies in the manuscript you have.

ADD REPLY • link 5.5 years ago by cpad0112 21k

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.cel files likely refer to miRNA data that was obtained from a microarray. You can't convert that type of data into fastq format which is sequence data.

ADD REPLY • link 5.5 years ago by GenoMax 141k

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So do I need another pipeline to analyze .cel file and make it a "sequence" file?

ADD REPLY • link 5.5 years ago by nkabo ▴ 80

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You can't make a sequence file from .cel. You will convert the intensity values into a numeric estimate which can then be used for data analysis. A primer here.

ADD REPLY • link 5.5 years ago by GenoMax 141k

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You first have to learn more about the method you are using before attempting analysis. No, microarray quantification cannot be converted to a file containing sequence data.

ADD REPLY • link 5.5 years ago by WouterDeCoster 47k

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