Transcriptome data handling

Question

[olga.lubinsky]

Hi,

I'm new in bioinformatics and i would really appreciate your help .

I'm trying to do an enrichment analysis.

1.I have a fasta file of the predicted proteins in my genome and a list of gene names that appear in the transcriptome. How can I make a FASTA file of the transcriptome?

2. I have a list of htseq-count, what statistical analysis is required in order to determine what gene are significantly expressed (i'm trying to determine my control transcriptome)

Thank you

[Devon Ryan]

Question #1 has the added complication that you're apparently starting with an amino acid sequence, which can be converted back to a rather large number of different DNA sequences. If you don't have much of a reference genome for your organism, then you might be better served by de novo assembly (e.g., with trinity).

[Ram]

Your question #1 needs more elaboration. What does the predicted protein have in common with the gene names?

Answer 1

[GouthamAtla]

Used egerR or DESeq to get list of DE genes.