RNA-SEQ on RICE

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3.3 years ago

Dr SKY ▴ 20

Hello , I am a beginner in RNA-Seq analysis. I am particularly working on Rice transcriptome using RNA-Seq pipeline. I have done DESeq2 analysis and have yielded DEG's for rice. I have found the list containing types of IDs 1) Os id 2) ENSRNA___ 3) EPlORYSAT__ and 4) gene- XYZ . I am confused on what other ids are all about? I am familiar with only the Os Id's Where from these id's have come? Which step and file has particularly produced it?

Will be grateful if someone can guide me.

RNA-Seq RICE TRANSCRIPTOMICS • 864 views

ADD COMMENT • link 3.3 years ago by Dr SKY ▴ 20

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Can you specify what software you used, and if relevent the transcriptome, annotation file, and/or genome assembly you used?

ADD REPLY • link 3.3 years ago by rpolicastro 13k

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Hello sir, Thank you for your response and kind concern.

I have used the following tools and files

Alignment : Hisat2 Counting : FeatureCounts

reff genome : Os-Nipponbare-Reference-IRGSP-1.0 rice plant genome from RAP-DB gtf: Os-Nipponbare-Reference-IRGSP-1.0 rice plant annotation file (gtf)

Will be glad if you can guide me towards clearing my confusion.

ADD REPLY • link 3.3 years ago by Dr SKY ▴ 20

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