009.4.R1.Translation.Rmd

---
title: "009.4.R1.Translation"
author: "qians"
date: "2022年2月24日"
output: html_document
---

```{bash}
cd /NAS/qians/Pseudogene/Data
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR180/006/SRR1802136/SRR1802136.fastq.gz
gunzip SRR1802136.fastq.gz
fastp -i SRR1802136.fastq -o SRR1802136.fastp.fastq --thread 8

wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR837/SRR837789/SRR837789.fastq.gz
gunzip SRR1802136.fastq.gz
for i in `ls *fastq`; do echo $i processed; fastp -i $i -o ${i%fastq}trim.fastq --thread 8; done

# map to tsRNA
## genome build
cat so_rna_type_namerRNA_AND_TAXONOMY9606_AND_rna_typerRNA_AND_entry_typeSequence.fasta tRNA_AND_so_rna_type_nameTRNA_AND_TAXONOMY9606_AND_rna_typetRNA_AND_entry_typeSequence.fasta > trRNA.fasta
bowtie2-build trRNA.fasta trRNA
## map
for i in `ls *trim.fastq`; do echo $i processed; bowtie2 -x ~/Pseudo/Data/Ref/Human/trRNA/trRNA -p 10 -U /NAS/qians/Pseudogene/Data/$i -S /NAS/qians/Pseudogene/Data/${i%fastq}sam --un-gz /NAS/qians/Pseudogene/Data/${i%fastq}tsRNAunaligned.fastq.gz; done

# map to genome
cd ~/Pseudo/Data/Ref/Human/bowtie2.index
#bowtie2-build Homo_sapiens.GRCh38.dna.primary_assembly.fa hg38
cd /NAS/qians/Pseudogene/Data
for i in `ls *.trim.tsRNAunaligned.fastq.gz`; do echo $i processed; bowtie2 -x ~/Pseudo/Data/Ref/Human/bowtie2.index/hg38 -p 10 -U /NAS/qians/Pseudogene/Data/$i -S /NAS/qians/Pseudogene/Data/${i%fastq.gz}Genomealigned.sam; done 

#sam to bam
for i in `ls *trim.tsRNAunaligned.Genomealigned.sam`; do echo $i processed; samtools view -Sb $i -q 20 -@ 10 | samtools sort -@ 10 -o ${i%sam}bam; done
for i in `ls *trim.tsRNAunaligned.Genomealigned.bam`; do echo $i processed; samtools index $i; done

#bam to bw
cd /NAS/qians/Pseudogene/Data
for i in `ls *bam`; do bamCoverage -b $i -bs 10 -p 10 --normalizeUsing RPKM -o ${i%bam}bw; done

```

# choose example
```{r}
S = "Human"
a = fread(file.path("~/Pseudo/Data/Seqdata/RPFdb",S,paste0(S,".all.RPKM.txt"))) %>% as.data.frame()
tmp = a[a$type!="Coding" & a$type!="lncRNA",c("Gene_ID","SRX273671","type")]
b = fread(file.path("~/Pseudo/Data/Ref",S,"gene.ENSG.name.2.txt"),header = FALSE) %>% as.data.frame()
tmp$type2 = b[match(tmp$Gene_ID,b$V1),2]
```