Question: CLIP-seq data process, start from sra file
1
gravatar for lin.pei26
5.2 years ago by
lin.pei26100
China
lin.pei26100 wrote:

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 • 1.9k views
ADD COMMENTlink modified 3.7 years ago by jimmy_zeng90 • written 5.2 years ago by lin.pei26100

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.

ADD REPLYlink written 3.7 years ago by jimmy_zeng90
0
gravatar for juncheng
5.2 years ago by
juncheng200
köln
juncheng200 wrote:

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

ADD COMMENTlink written 5.2 years ago by juncheng200
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