Differentially expressed genes

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#1

Hi,
I have two assembled fasta files, one for control and second for disease condition. I need to fine differentially expressed genes in both of them. Plz guide me how to perform this type of analysis.
Regards

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#2

Hi @humaira,
it depends on the goal of your analysis and the type of data you have. When you talk about assembled fasta files, you mean assembled transcriptomes generated by RNA-seq?

Regards

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#3

You have two Fasta or FASTQ files ? FASTA are for references. I assume you have 2 FASTQ files between two conditions. If this is true, you should align it with HISAT2 then Featurecount for quantification and Use deseq2 or edgeR for DEG. Other tools are useful too.

Best

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#4

I have two fasta files. one for normal and second for diseased condition.

#5

how many repeats do you have for each condition ?

Best

#6

AOA.
133,900 reads for normal and 132,900 for diseased.

Regards.

#7

you are telling the number of your reads. i meant the number of your datasets
You can use your fastas as reference genome not your main samples as i think i told you before. i assume you build your reference genome.
Whats your analysis about? is it in homo sapiens fields or else ?!

#8

I am working on transcriptome analysis of plant and no reference genome exists for this plant.

#9

yes assembled transcriptomes generated by RNA-seq.

#10

Hi @humaira,
you can use Salmon Quant for performing the differential expression analysis. I recommend you to have a look at this tutorial: Quantification of gene expression: Salmon.

Regards

#11

Hi.
Thx. now i need to separate differentially expressed transcripts from both fasta files. Guide me plz.

regards

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#12

Here is a very useful tutorial for assembly and differential expression of de novo transcriptomes. It should walk you through the whole process. :slightly_smiling_face:

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#13

9 posts were split to a new topic: Troubleshooting problems with DESeq2