Question: Merge DEseq and Cufflinks outputs
gravatar for Lissa Cruz Saavedra
11 months ago by
Lissa Cruz Saavedra0 wrote:

Hi everyone

I am trying to get a very cofidence results from RNAseq data. I was reading about compare or merge between different diferential expression test outputs as DEseq and Cufflinks, but I am wondering about how could iI do it. because i will a lot ID genes from my DEGs.

Thanks a lot!

rna-seq deseq degs cufflinks • 293 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by Lissa Cruz Saavedra0

I did compared DESeq2 vs Tuxedo suit, (In general bioinformaticians suggest to don't use use cufflinks but the updated pipeline, HISAT2 > StringTIE > Ballgown). Once you get your results, removed the ID with high p-value for each output, then you can use the Venny Graph to see what is common and what is not. I hope this help,

I was surprised about the result, only 6% of overlapped genes

ADD REPLYlink modified 11 months ago • written 11 months ago by Morris_Chair190

Hi, I am sorry to be late.

You mean I coul take the reads from DEGs in my bam file from each on my statistic softwares?

ADD REPLYlink written 11 months ago by Lissa Cruz Saavedra0

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is only for new answers to the original question. This comment belongs under @Kevin's answer.

ADD REPLYlink written 11 months ago by genomax85k
gravatar for Kevin Blighe
11 months ago by
Kevin Blighe61k
University College London
Kevin Blighe61k wrote:

If you just want to use the test statistics (p-values, fold-changes, etc) from Cufflinks and DESeq2, then I would aim to perform what is called a 'meta analysis'.

Otherwise, I would retrieve the raw data (FASTQ or BAM) from both experiments and re-process everything myself using the same pipeline.


ADD COMMENTlink written 11 months ago by Kevin Blighe61k
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