CLIP-seq data process, start from sra file

Question

[Pei]

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

[jimmy_zeng]

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.

Answer 1

[juncheng]

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