Using RSEM reads for DESeq2
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deeptiptl74 ▴ 10
@deeptiptl74-13880
Last seen 14 months ago

Hi,

I am new to the Bioinformatics. I want to find differentially expressed genes from a non model species. I used trinity for the de novo assembly and used RSEM to count the reads. I used fastq files as input for RSEM not bam files (sorted by name). In the DESeq2 manual it says, name sorted bam files are necessary to run the analysis for paired end reads, So can I use the RSEM output that I have, for DESeq2 or not? 

Thank you so much for your time and help.

Deepti

deseq2 rsem • 646 views
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@mikelove
Last seen 2 days ago
United States

hi Deepti,

See the tximport package for importing the estimated counts per gene from RSEM, and then you can use DESeqDataSetFromTximport() to begin the DESeq2 analysis.

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Thanks Michael.

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