Hello ,
I am new to RNA-seq and can anyone guide me on how to do analysis on my data? I know I need to write a script to select my data based p-values and Q values for differential expression, but I do not know how to do it. Can I write the script on bash? or Do I need python or R? and if so, can some guide me on that?
Thanks,
Regards,
Aynur Erkin if you are using the tophat-cufflink pipeline. I would suggest you, not to use it. Even the author is not suggesting. I would recommend DEseq2 and EdgeR (star-based) or use star or hisat2 instead of the tophat.
https://www.biostars.org/p/357060/
Hi thanks for your answer. I was learning through practicing one article and they used top hat but I’have sue STAR and I wanna continue from cuffdiff diff.exp.genes to plot the results.
If you just need to select the genes that meet certain p and q value criteria, then learn the unix command awk. Use the redirect symbol ">" to write outputs to a file. In the long run, you should learn to use R, as this will allow you to import your cuff-diff file (or any other DE analysis file) and select/plot/analyze whatever data you like.
Just open your differential expression result file in Excel or any other office based on your operating system which you are using. You can use simple filters to retrieve DEG's.
- Badges
- Science topic
- Similar topics
- Linguistics
- Composition Studies
- Writing