CLIP-seq data process, start from sra file
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7.0 years ago
Pei ▴ 130

Hi all:

I am trying to re-analyzed a CLIP-SEQ dataset, downloaded from GEO: SRR048973(GSM545212)

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM545212

After downloading the sra file (unaligned), I used fastq-dump to converse this file into fastq format.

Can/Should I now use Bowtie to generate aligned SAM file ?

 

Thanks in advance!

Best,

CLIP • 2.4k views
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Have you done the whole pipeline for the Chiq-seq data ? I am new to epigenomic data analysis and also want to process the data you just mention . we counld talk more about this.

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7.0 years ago
juncheng ▴ 200

Yes, you can. And if you want further analysis, you need to do mapping.

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