Question: mapping of rna seq read to reference seq
0
gravatar for fatimarasool135
23 months ago by
fatimarasool13560 wrote:

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

rna-seq • 1.1k views
ADD COMMENTlink modified 23 months ago by WouterDeCoster44k • written 23 months ago by fatimarasool13560
3
gravatar for WouterDeCoster
23 months ago by
Belgium
WouterDeCoster44k wrote:

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.

ADD COMMENTlink written 23 months ago by WouterDeCoster44k
1

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

ADD REPLYlink written 23 months ago by ATpoint40k

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

ADD REPLYlink written 23 months ago by fatimarasool13560
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