Gene function for wheat
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4.5 years ago

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 • 1.1k views
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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.

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

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I got all these genes ID from Ballgown under bioconductor

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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