Question: Gene function for wheat
0
gravatar for fahad.otb
11 months ago by
fahad.otb0
United States
fahad.otb0 wrote:

Hello everyone, How can I know the gene function for up and down regulated wheat genes?. For example:

MSTRG.132410
MSTRG.151360
MSTRG.39782
MSTRG.59628
MSTRG.107728
MSTRG.29810
MSTRG.49682
MSTRG.98238
MSTRG.139990

Thanks

rna-seq • 412 views
ADD COMMENTlink modified 10 months ago by Biostar ♦♦ 20 • written 11 months ago by fahad.otb0
1

Did you use any standard GTF (eg. Ensembl, NCBI, UCSF)? MSRTG are assigned by ballgown within each sample and can't be compared across samples. You need to take out the coordinates and search for the genes/transcripts within those coordinates and work with them. If there is no match, then they are novel/unidentified/unknown genes/transcripts in your data.

ADD REPLYlink modified 11 months ago • written 11 months ago by cpad01129.3k

Where did those ID's come from? They don't appear to be standard gene identifiers for wheat.

ADD REPLYlink modified 11 months ago • written 11 months ago by genomax57k

I got all these genes ID from Ballgown under bioconductor

ADD REPLYlink written 11 months ago by fahad.otb0

Use a reference GTF file to map first before going for ballgown. If you had used and still get these ids, these are novel ones as mentioned above

ADD REPLYlink written 10 months ago by pixie@bioinfo1.3k
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