CLIP-seq data process, start from sra file

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

• 3,701 views • link

updated 4.4 years ago by Ram

• written 11.6 years ago by Pei

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.

• 1 views • link

written 10.2 years ago by jimmy_zeng

1 answer

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

• 0 views • link

written 11.6 years ago by juncheng

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