Transcriptome data handling · Biostar

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Transcriptome data handling

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

trasnscriptome enrichment

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updated 11.6 years ago by Ram

• written 11.6 years ago by olga.lubinsky •

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

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written 11.6 years ago by Ram

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).

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written 11.6 years ago by Devon Ryan

1 answer

Used egerR or DESeq to get list of DE genes.

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written 11.6 years ago by GouthamAtla

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