software after human STAR mapping

Question

[yueli7]

Hello,

I have already finished mapping reads to the huamn genome by STAR.

Which software I can use for transcript abundance estiamtes or Alignment/Junction?

Cufflinkd, StringTie, RSEM, Miso, TIGAR, simple?

Any suggestions are appreciated!

[WouterDeCoster]

Please select a more descriptive title for your thread, for example: "human transcript abundance estimation after STAR mapping".

[yueli7]

Thanks for Bastien Herve quick response!

I just want to find out the differential expressed genes in human genome after STAR.

Which software is suitable for RNA-seq?

Any suggestions are appreciated!

[Bastien Hervé]

What are you thinking when you said "software" ? To get "the differential expressed genes", first, after the alignment of your reads on a reference genome (like you did with STAR), you need to count how many reads mapped your genes (featureCounts is a tool to do that). Then you need to normalize your count (size between libraries etc...), and only after this step you can do your differential expression analyze. Last two steps can be done with DESeq2 tool.

[GenoMax]

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

@Bastien has already given you pointers for software you can use to address your question.

Those will work fine for gene level DE analysis.

Answer 1

[Bastien Hervé]

Depends on what you want to achieve after, you will have to read the documentation of each software if you want something really specific.

As your post is a general question, if you want, by example, a heatmap of your down/up regulated genes, after STAR you can go to featureCounts or HTSeq-count.

You will got a genes count file. Then run DESeq2 on it to normalize your data and create your heatmap.