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Using MapMan

Wheat RNAseq data

Wheat RNAseq data
答复
18-12-21 下午8:32
Hello,
I have wheat RNAseq data with Gene ID such as Traes_5AS_083EC1177. I have installed a Mapman mapping file named “IWGSP_MIPSv2.2”. I found that, in this mapping file Gene IDs are like “traes_5bs_324938cad.1
How do I “convert” my Gene IDs so that I it is compatible with this Mapman file ?

RE: Wheat RNAseq data
答复
18-12-24 下午3:25 回复Prasun Ray。
Hi
with the latest MapMan x4 version we switched to ENSEMBL identifiers. They also start with Traes but then seem to look different. Now if you did use ensemble use evertyhing that starts with X4 if not since you used RNAseq you should have either [1] trascripts fastas (salmon/kallisto) or [2] genome + gff (hisat/bwa/bowtie etc) pipelines.
If so [1] use the transcripts in Mercator (it only takes a few minutes to get your MapMan annotation file if [2] use genome + gff file to create [1]e.g. by using gffread

Best Wishes
Björn

RE: Wheat RNAseq data
答复
18-12-25 下午4:23 回复Björn Usadel。
Hi Björn,
Thank you for your reply.
By the way, from where do I download MapMan x4 version.
Thank You,
Prasun Ray