Question: mapping of rna seq read to reference seq
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gravatar for fatimarasool135
6 months ago by
fatimarasool13520 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 • 330 views
ADD COMMENTlink modified 6 months ago by WouterDeCoster39k • written 6 months ago by fatimarasool13520
3
gravatar for WouterDeCoster
6 months ago by
Belgium
WouterDeCoster39k 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 6 months ago by WouterDeCoster39k
1

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

ADD REPLYlink written 6 months ago by ATpoint17k

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 6 months ago by fatimarasool13520
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