Merge DEseq and Cufflinks outputs

Question

[Lissa Cruz Saavedra]

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!

[Morris_Chair]

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,

https://bioinfogp.cnb.csic.es/tools/venny/

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

[Lissa Cruz Saavedra]

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?

[GenoMax]

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.

Answer 1

[Kevin Blighe]

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.

Kevin