Question: RNAseq data analysis using cufflinks
gravatar for Gyan prakash Mishra
3.3 years ago by
Gyan prakash Mishra0 wrote:

Hi all,

I am analyzing RNAseq data using cufflinks but I have some confusion regarding the the flow of analysis.

I have RNAseq data for 4 condition say A,B,C and D each having 2 replicate say R1 and R2.

steps which I am following

1. Mapped the reads(using bowtie2) ---> output : 8 aligned sam and bam file(A_R1, A_R2, B_R1 , B_R2.......)

2.  cufflink (e.g : cufflink -o A_R1 -G mm10 A_R1) ----> output : 8 transcript.gtf (A_R1.gtf, A_R2.gtf......)

3. cuffmerge (e.g Cuffmerge -o A -g mm10 assembly _GTF_list.txt) . assembly _GTF_list.txt has list of transcript.gtf for each replicate (for e.g A_R1.gtf and A_R2.gtf) ----> output : merged.gtf

Now i have 4 merged.gtf for 4 condition.

First of all I would like to know wheather I am going in right direction or not and secondly I am confused with the use of cuffquant and cuffdiff. I will appreciate any help.

Thanks in advance!




cufflinks • 1.4k views
ADD COMMENTlink modified 3.3 years ago by Devon Ryan1.9k • written 3.3 years ago by Gyan prakash Mishra0
gravatar for Devon Ryan
3.3 years ago by
Devon Ryan1.9k
Devon Ryan1.9k wrote:

You're close. For step 3 you need to merge the GTF files for all samples across all groups so you end up with a single merged GTF file for everything.

ADD COMMENTlink written 3.3 years ago by Devon Ryan1.9k
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