Don't know how to analysis the downloaded data from ENCODE project, including tsv file about gene quantification and transcript quantification
0
0
Entering edit mode
4.9 years ago

Recently, I downloaded some rna-seq data about hESC and want to find out the specific gene expressed in hESCs rather than other cell type(Also download rna-seq data about fibroblast.). Both data file types are tsv. I am really fresh to data analysis, so forgive me for such boring questions maybe.

RNA-Seq • 2.3k views
ADD COMMENT
0
Entering edit mode

I think it is better to give some data in the TSV file so that we can understand what type of data is in the TSV file. Depend on the TSV data, maybe we can give some hint how to process the data.

ADD REPLY
0
Entering edit mode

the tsv data mainly including following parts: gene_id, transcript_id, length, effective length, expected_count, TPM, FPKM and several others. I think it is like the data had already been processed and need visualization or what.

ADD REPLY
1
Entering edit mode

I see. So, you can directly use the data for expression analysis. For example, you can use the expected count as input for DESeq2. Useful keyword for studying is differential expression analysis.

ADD REPLY
0
Entering edit mode

Got it. Really appreciate it.

ADD REPLY

Login before adding your answer.

Traffic: 3112 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6