Question: mapping of rna seq read to reference seq
0
gravatar for fatimarasool135
9 days ago by
fatimarasool1350 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 • 132 views
ADD COMMENTlink modified 9 days ago by WouterDeCoster35k • written 9 days ago by fatimarasool1350
3
gravatar for WouterDeCoster
9 days ago by
Belgium
WouterDeCoster35k 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 9 days ago by WouterDeCoster35k
1

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

ADD REPLYlink written 9 days ago by ATpoint10k

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 5 days ago by fatimarasool1350
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1078 users visited in the last hour