Question: (Closed) Which Software Can Map Tags To Genes And Calculate Their Differential Expression
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gravatar for gaojian8888
4.6 years ago by
gaojian88880 wrote:

How to map tags to genes and calculate their differential expression, which software should I use, including the cDNA database, I do research in Maize

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ADD COMMENTlink modified 4.6 years ago by Istvan Albert ♦♦ 75k • written 4.6 years ago by gaojian88880
1

which kind of tags? this question is currently far too vague and possible duplicate of: RNA-seq pipeline, RNAseq differential expression , How to calculate differential gene expression in RNAseq experiments?, Survey: RNA-Seq analysis for Differential Gene/Transcript Expression [updated with results] and many more

please provide more details if it is not standard RNA-seq

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by Michael Dondrup43k

Hi Michael, I got the DGE(digital gene expression) clean tags ( it is only 21bp), I want to map these clean tags to genes( cDNA is OK?), I try to use bwa but the result is match zero, because my tags file is txt formation? so can you tell me which software will be best for choose and how to map these tags, I do research in maize, all the cDNA database is download from the website.

ADD REPLYlink written 4.6 years ago by gaojian88880

It is showed below like this CATGAAAAAAAAAAAAAAAAA CATGAAAAAAAAAAAAAAAAC CATGAAAAAAAAAAAAAAACA CATGAAAAAAAAAAAAAAATT CATGAAAAAAAAAAAAAAGAA CATGAAAAAAAAAAAAAATAA CATGAAAAAAAAAAAAACAAA CATGAAAAAAAAAAAAACATC CATGAAAAAAAAAAAAAGAAA CATGAAAAAAAAAAAACAAAA CATGAAAAAAAAAAAAGAAAA

ADD REPLYlink written 4.6 years ago by gaojian88880
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