a3.denovo.md

Ribo-seq : De novo annotation (RiboCode)

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Workflow

Data:

STAR mapping (Aligned.toTranscriptome.out.bam) RPF with 3nt periodicity

Key words:

P-sites and Offset

Step:

STAR mapping DONE!

• Step 1 : Install/Upgrade RiboCode
• Step 2 : Prepare transcripts annotation
• Step 3 : Select RPF length and detect P-site offset
• Step 4 : Detect translated ORFs

Step 1 : Install/Upgrade RiboCode

	pip install --upgrade RiboCode
		------------------------------------
		ssh -p 2200 [email protected]
		# password: yanglab62783319
		cd ~/Ribo-seq_Pipeline/RiboCode
		------------------------------------
		/workdata2/Programs/anaconda3/bin/RiboCode

Step 2 : Prepare transcripts annotation

	prepare_transcripts -g <gencode.v19.annotation.gtf> -f <hg19_genome.fa> -o <RiboCode_annot>
		|1| transcripts_cds.txt
		|2| transcripts.pickle
		|3| transcripts_sequence.fa

Step 3 : Select RPF length and detect P-site offset

	metaplots -a <RiboCode_annot> -r <HEK293Aligned.toTranscriptome.out.bam>

Metaplots

Config File

RiboCode: Key words

Step 4 : Detect translated ORFs

RiboCode -a <RiboCode_annot> -c <config.txt> -l no -o <RiboCode_ORFs_result>

pie plot

Detected ORFs Files

<RiboCode_ORFs_result>.txt <RiboCode_ORFs_result>_collapsed.txt

code

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