RNA Types in Genome

Files curated and organized by Yuhuan

Reference bed files: /BioII/lulab_b/taoyuhuan/RNA_biotype/bed_by_biotype

如何获取常见基因/RNA类型的注释信息

0. Total RNA Clean Reads V.S. Human Transcriptome

• I. Total RNA Clean Reads (rRNA depleted) = Clean Reads (remove adaptor and short reads) - spikeIn - Univec - nucleus_rRNA - Mt_rRNA

  • (1) Mapped to Human Nucleus Genome

  • (2) Mapped to MT Genome

  • (3) Mapped to Microbial Genomes

  • (4) Unmapped

• II. Human Transcriptome see the following section 2-3

1. Mitocondrial Transcriptome

Mitocondrial_Transcriptome	Definition	Biotype or name annotation in gtf	Command for gtf_by_biotype	Note	Command for gtf2bed
MT_tRNA		transcript_type "Mt_tRNA"	awk -F "\t" '$3=="exon"' ../gtf/gencode.gtf | grep 'transcript_type "Mt_tRNA' > MT_tRNA.gtf		awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' MT_tRNA.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/MT_tRNA.bed
MT_lncRNA		transcript_type "Mt_lncRNA"	awk -F "\t" '$3=="exon"' ../gtf/gencode.gtf	grep 'transcript_type "3prime_overlapping_ncRNA|transcript_type "antisense|transcript_type "bidirectional_promoter_lncRNA|transcript_type "lincRNA|transcript_type "macro_lncRNA|transcript_type "non_coding|transcript_type "processed_transcript|transcript_type "sense_intronic|transcript_type "sense_overlapping'	grep chrM > MT_lncRNA_gencode.gtf; awk -F "\t" '$3=="exon"' ../gtf/mitranscriptome.gtf | grep 'tcat "lncrna' | grep chrM > MT_lncRNA_mitranscriptome.gtf; cat MT_lncRNA_gencode.gtf MT_lncRNA_mitranscriptome.gtf > MT_lncRNA.gtf		awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' MT_lncRNA_gencode.gtf	sed 's/gene_id //g'	tr -d '"' > ../bed_by_biotype/MT_lncRNA_gencode.bed; awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[3],0,$7}' MT_lncRNA_mitranscriptome.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/MT_lncRNA_mitranscriptome.bed; cat ../bed_by_biotype/MT_lncRNA_gencode.bed ../bed_by_biotype/MT_lncRNA_mitranscriptome.bed > ../bed_by_biotype/MT_lncRNA.bed
MT_mRNA		transcript_type "Mt_mRNA"	awk -F "\t" '$3=="exon"' ../gtf/gencode.gtf | grep 'transcript_type "protein_coding' | grep chrM > MT_mRNA.gtf		awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' MT_mRNA.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/MT_mRNA.bed
Note: MT_exon (for reference, not included)		$3=="exon"	awk -F "\t" '$3=="exon"' ../gtf/gencode.gtf	grep chrM > MT_exon_gencode.gtf; awk -F "\t" '$3=="exon"' ../gtf/mitranscriptome.gtf | grep chrM > MT_exon_mitranscriptome.gtf; cat MT_exon_gencode.gtf MT_exon_mitranscriptome.gtf > MT_exon.gtf	tcat "mixed_read_through"	awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' MT_exon_gencode.gtf	sed 's/gene_id //g'	tr -d '"' > ../bed_by_biotype/MT_exon_gencode.bed; awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[3],0,$7}' MT_exon_mitranscriptome.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/MT_exon_mitranscriptome.bed; cat ../bed_by_biotype/MT_exon_gencode.bed ../bed_by_biotype/MT_exon_mitranscriptome.bed > ../bed_by_biotype/MT_exon.bed
Note: MT_rRNA (need to be revmoed)		transcript_type "Mt_rRNA"	awk -F "\t" '$3=="exon"' ../gtf/gencode.gtf | grep 'transcript_type "Mt_rRNA' > MT_rRNA.gtf		awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' MT_rRNA.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/MT_rRNA.bed

2. Human Transcriptome for common usage

Human_Transcriptome for common usage	Definition	Biotype or name annotation in gtf	Command for gtf_by_biotype	Note	Command for gtf2bed
lncRNA	Generic long non-coding RNA biotype that replaced the following biotypes: 3prime_overlapping_ncRNA, antisense, bidirectional_promoter_lncRNA, lincRNA, macro_lncRNA, non_coding, processed_transcript, sense_intronic and sense_overlapping.	transcript_type "3prime_overlapping_ncRNA", transcript_type "antisense", transcript_type "bidirectional_promoter_lncRNA", transcript_type "lincRNA", transcript_type "macro_lncRNA", transcript_type "non_coding", transcript_type "processed_transcript", transcript_type "sense_intronic", transcript_type "sense_overlapping", tcat "lncrna"	awk -F "\t" '$3=="exon"' ../gtf/gencode.gtf	grep 'transcript_type "3prime_overlapping_ncRNA|transcript_type "antisense|transcript_type "bidirectional_promoter_lncRNA|transcript_type "lincRNA|transcript_type "macro_lncRNA|transcript_type "non_coding|transcript_type "processed_transcript|transcript_type "sense_intronic|transcript_type "sense_overlapping'	grep -v chrM > lncRNA_gencode.gtf; awk -F "\t" '$3=="exon"' ../gtf/mitranscriptome.gtf | grep 'tcat "lncrna' | grep -v chrM > lncRNA_mitranscriptome.gtf; cat lncRNA_gencode.gtf lncRNA_mitranscriptome.gtf > lncRNA.gtf		awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' lncRNA_gencode.gtf	sed 's/gene_id //g'	tr -d '"' > ../bed_by_biotype/lncRNA_gencode.bed; awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[3],0,$7}' lncRNA_mitranscriptome.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/lncRNA_mitranscriptome.bed; cat ../bed_by_biotype/lncRNA_gencode.bed ../bed_by_biotype/lncRNA_mitranscriptome.bed > ../bed_by_biotype/lncRNA.bed
mRNA		transcript_type "protein_coding"	awk -F "\t" '$3=="exon"' ../gtf/gencode.gtf | grep 'transcript_type "protein_coding' | grep -v chrM > mRNA.gtf		awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' mRNA.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/mRNA.bed
pseudogene	Have homology to proteins but generally suffer from a disrupted coding sequence and an active homologous gene can be found at another locus. Sometimes these entries have an intact coding sequence or an open but truncated ORF, in which case there is other evidence used (for example genomic polyA stretches at the 3' end) to classify them as a pseudogene. Can be further classified as one of the following: processed_pseudogene, polymorphic_pseudogene, retrotransposed, transcribed_processed_pseudogene, transcribed_unprocessed_pseudogene, transcribed_unitary_pseudogene, translated_processed_pseudogene, translated_unprocessed_pseudogene, unitary_pseudogene, unprocessed_pseudogene.	transcript_type "polymorphic_pseudogene", transcript_type "processed_pseudogene", transcript_type "retrotransposed",transcript_type "transcribed_processed_pseudogene", transcript_type "transcribed_unitary_pseudogene", transcript_type "transcribed_unprocessed_pseudogene", transcript_type "translated_processed_pseudogene", transcript_type "translated_unprocessed_pseudogene", transcript_type "unitary_pseudogene", transcript_type "unprocessed_pseudogene"	awk -F '\t' '$3=="exon"' ../gtf/gencode.gtf | grep 'transcript_type "polymorphic_pseudogene|transcript_type "processed_pseudogene|transcript_type "retrotransposed|transcript_type "transcribed_processed_pseudogene|transcript_type "transcribed_unitary_pseudogene|transcript_type "transcribed_unprocessed_pseudogene|transcript_type "translated_processed_pseudogene|transcript_type "translated_unprocessed_pseudogene|transcript_type "unitary_pseudogene|transcript_type "unprocessed_pseudogene' > pseudogene.gtf		awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' pseudogene.gtf | sed 's/gene_id //g' | tr -d '"' > pseudogene.bed
snoRNA		transcript_type "snoRNA"	awk -F "\t" '$3=="exon"' ../gtf/gencode.gtf | grep 'transcript_type "snoRNA' > snoRNA.gtf		awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' snoRNA.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/snoRNA.bed
snRNA		transcript_type "snRNA"	awk -F "\t" '$3=="exon"' ../gtf/gencode.gtf | grep 'transcript_type "snRNA' > snRNA.gtf		awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' snRNA.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/snRNA.bed
srpRNA		gene_name "RN7SL*"	awk -F "\t" '$3=="exon"' ../gtf/gencode.gtf | grep 'gene_name "RN7SL' > srpRNA.gtf	belong to misc_RNA	awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' srpRNA.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/srpRNA.bed
tRNA		gene_type "Pseudo_tRNA"	gencode_tRNA.gtf		awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' gencode_tRNA.gtf | sed 's/gene_id //g' | tr -d '"' | sed '1,5d' | grep -v chrM > ../bed_by_biotype/tRNA.bed
Y_RNA		gene_name "Y_RNA"	awk -F "\t" '$3=="exon"' ../gtf/gencode.gtf | grep 'gene_name "Y_RNA' > Y_RNA.gtf	belong to misc_RNA	awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' Y_RNA.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/Y_RNA.bed
misc (extract srpRNA, YRNA independently, the others may be ignored sometimes)	misc_RNA + ribozyme + scaRNA + vaultRNA/vault_RNA etc	misc_RNA: 7SK etc (need to remove Xiist etc)	-	-	-
tucpRNA		tcat "tucp"	awk -F "\t" '$3=="exon"' ../gtf/mitranscriptome.gtf | grep 'tcat "tucp' > tucpRNA.gtf		awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[3],0,$7}' tucpRNA.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/tucpRNA.bed
circRNA
Note: exon (for reference, not included)		$3=="exon"	awk -F "\t" '$3=="exon"' ../gtf/gencode.gtf	grep -v chrM > exon_gencode.gtf; awk -F "\t" '$3=="exon"' ../gtf/mitranscriptome.gtf | grep -v chrM > exon_mitranscriptome.gtf; cat exon_gencode.gtf exon_mitranscriptome.gtf > exon.gtf		awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[1],0,$7}' exon_gencode.gtf	sed 's/gene_id //g'	tr -d '"' > ../bed_by_biotype/exon_gencode.bed; awk 'BEGIN{FS="\t";OFS="\t"}{split($9,a,";");print $1,$4-1,$5,a[3],0,$7}' exon_mitranscriptome.gtf | sed 's/gene_id //g' | tr -d '"' > ../bed_by_biotype/exon_mitranscriptome.bed; cat ../bed_by_biotype/exon_gencode.bed ../bed_by_biotype/exon_mitranscriptome.bed > ../bed_by_biotype/exon.bed

3. More Potential Human RNAs

More Potential Human RNAs	Definition	Biotype or name annotation in gtf	Command for gtf_by_biotype	Note	Command for gtf2bed
enhancer
repeats
promoter