The difference of RNA-seq data between TCGA and ENCODE

Question

[dao]

Hi All,

I'm new to RNAseq, so I'm confused with a couple of terms. Now, I have questions about RNA-seq data from different databases.

1. the first is from TCGA, columns include:

gene_id gene_name gene_type unstranded stranded_first stranded_second tpm_unstranded fpkm_unstranded fpkm_uq_unstranded

1. the seconde is from ENCODE, columns include:

gene_id transcript_id(s) length effective_length expected_count TPM FPKM posterior_mean_count posterior_standard_deviation_of_count pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound FPKM_ci_lower_bound FPKM_ci_upper_bound

My question is: Do the two files have equivalent parameters (column names)?

I am really confused, and please help. Thanks in advance.

Best regards,

Dao

[DareDevil]

TCGA and ENCODE are two different databases (projects) and they follow different naming convensions.

The counts given in TCGA (V32) are based STAR pipeline

[dao]

Hi, Thanks for your answer, I would like to know if there is a tool that can be used for format conversion?

[DareDevil]

here you can not convert.