utterances-bot commented 8 months ago

Genomics web - Pipeline de Genómica en R

https://franciscoascue.github.io/Rgenomics/modulo8.1.html

FranciscoAscue commented 8 months ago

Para los que tengar error en Rbowtie2

En la terminal WSL ejecutar lo siguiente:

## moverse a referencia 
cd data/referencia

## Instalar bowtie2
sudo apt install bowtie2

## bowtie2-build 
bowtie2-build GCF_000085865.1_ASM8586v1_genomic.fna index/myco

FranciscoAscue commented 8 months ago

source("install.R", local = TRUE)

# Source scripts
library(R.utils) # Linux 

source("scripts/sratoolkit.R", local = TRUE)
source("scripts/listfastq.R", local = TRUE)
source("scripts/filtereads.R", local = TRUE) 
source("scripts/consensus.R", local = TRUE) 

############### Download genomes from NCBI ###############
##########################################################

url <- fromJSON(file = "data/reference/ref.json")
filename <- "GCF_000085865.1_ASM8586v1_genomic.fna.gz"
download_genome(url$urlref,filename, "data/reference/")

############### Download files from SRA - NCBI ###############
##############################################################

download_sra_files(id = "SRR15616380")
download_sra_files(id = "SRR15616379")

############### Quality of fastq ###############
################################################

lecturas <- list_fastq(pattern = c("SRR15616379_1.fastq","SRR15616379_2.fastq"))
plotQualityProfile(c(lecturas$lf,lecturas$lr))

## Adicional

library(fastqcr)
fastqc(fq.dir = "data/rawdata/", # Directorio de archivos FASTQ
       qc.dir = "results/", # Directorio de resultados
       threads = 4,
       fastqc.path = "FastQC/fastqc"
)

qc.dir = "results/"
qc_report(qc.dir, result.file = "results/multiqc/",
          experiment = "Mycoplasma")

############### Filter reads from fastq files ###############
#############################################################

log_filter <- filter_reads(name = lecturas$name, lf = lecturas$lf, 
             lr = lecturas$lr, trunc = 250)

############### Assembly genomes ###############
################################################

# uncompressed reference genome 
gunzip("data/reference/GCF_000085865.1_ASM8586v1_genomic.fna.gz")

# reference genome bowtie2 index 
bowtie2_build("data/reference/GCF_000085865.1_ASM8586v1_genomic.fna",
              bt2Index = "data/reference/index/myco" , overwrite = TRUE)

# aling fastq files to reference 

bowtie2(bt2Index = "data/reference/index/myco", 
        samOutput = "results/SRR15616379.sam", 
        seq1 = "data/processed_data/filtered_F/SRR15616379_filt_1.fastq", 
        seq2 = "data/processed_data/filtered_R/SRR15616379_filt_2.fastq", 
        "--threads=3")

############### Alignment files manipulation ###############
############################################################

# Convert to BAM files

asBam("results/SRR15616379.sam")

# Read BAM file

bamFile <- BamFile("results/SRR15616379.bam")

# Statistics of alignment  

bam <- countBam(bamFile)
quickBamFlagSummary(bamFile)
seqinfo(bamFile)

# Open large size of BAM files 

yieldSize(bamFile) <- 1
open(bamFile)
scanBam(bamFile)[[1]]$seq
close(bamFile)
yieldSize(bamFile) <- NA

CevicheConPalta commented 8 months ago

https://strawberryperl.com/

CarolaMP commented 7 months ago

Buenas noches profesor, cuando intento correr este comando me sale error y no se porque:

library(fastqcr) fastqc(fq.dir="data/rawdata/",

qc.dir="results/",

threads = 4,

fastqc.path = "FastQC/fastqc") Error in .check_if_unix() : Unix system (MAC OSX or Linux) required.

FranciscoAscue commented 7 months ago

@CarolaMP Que tal Carola, ese error lo mencione en clase que podia ser posible, por ello revisa como realizar ese analisis pero desde la terminal.

#sudo apt install fastqc
fastqc -t 4 -o results/ data/rawdata/*fastq.gz

FranciscoAscue commented 6 months ago

LINK PARA EMSAMBLAJE PARA TERMINAL

IVANmt7 commented 5 months ago

Hola Francisco, tienes una solución para el siguiente error al momento de alinear con Bowtie2 los índices del genoma de referencia con los filtrados de los reads?: (¿tal vez una alternativa en la terminal?)

bowtie2(bt2Index = "data/reference/index/myco",

samOutput = "results/SRR15616379.sam",

seq1 = "data/processed_data/filtered_F/SRR15616379_filt_1.fastq",

seq2 = "data/processed_data/filtered_R/SRR15616379_filt_2.fastq",

"--threads=3") Error in system(call, intern = TRUE, show.output.on.console = TRUE) : 'perl' not found

srm78d commented 3 months ago

Aní me pasa igual,

Error in system(call, intern = TRUE, show.output.on.console = TRUE) : 'perl' not found

pieronimbus commented 3 months ago

Entrega de Trabajo

Integrantes: Piero Araujo Chávez

5 "Modulo8"

Rplot

Código:

ggplot(cover, aes(x = pos, y = count, color = count)) + geom_point(shape = ".", size = 1) + scale_color_gradient(low = "lightblue", high = "darkred") + labs(title = "Gráfico de Cobertura", subtitle = "Gráfico de Cobertura de Genoma 'Metamycoplasma hominis'", x = "Posición", y = "Cobertura") + theme_minimal() + theme(plot.title = element_text(hjust = 0.5), plot.subtitle = element_text(hjust = 0.5)) + annotate("text", x = Inf, y = -Inf, hjust = 1, vjust = -1, label = "Autor: Piero Martín Araujo Chávez", size = 3)

FranciscoAscue / Rgenomics