mapping of rna seq read to reference seq

Question

[fatimarasool135]

Hi. what will be the reference sequence used for mapping of rna seq read to reference ? shuold it be cDNA or genomic sequence?

Answer 1

[WouterDeCoster]

You did not tell us anything about your organism, your technology or the aim of your analysis, but most commonly you will align to the genomic sequence, using a spliced aligner such as STAR or HISAT2 in case of an eukaryotic organism. There are also pseudoalignment tools such as kallisto and salmon which use the transcriptome (cDNA). It also depends on how well your annotation and assembly is.

[ATpoint]

In any case, you might consider to read this guide to get a proper background before diving into any analysis.

[fatimarasool135]

i am working on wheat rna seq . i want to get specific gene / transcript from it.kindly tell me steps for this analysis