Hello Everyone, 
I'm new to RNAseq world and Rstudio in general and I want to analyze a couple of bamfiles from illumina. 
So far, I successfully followed tutorials for the analysis of RNAseq like this:

https://master.bioconductor.org/help/course-materials/2016/CSAMA/lab-3-rnaseq/rnaseq_gene_CSAMA2016.html


Unfortunately, all the tutorials available start by giving packages and descriptions about how to import into R but none of them shows how to import bamfiles not packaged.

I learned about how to  look into bamfile for example by running this commands:

library(Rsamtools)

bam1 <-"test.bam"
bam1 <-scanBam("test.bam")

bam1

so that I can look what's inside but after that I'm stopped because I don't know how to proceed. 
I would be super happy to receive some help, just for one step forward.

Thank you very much 

P

To import data from bam files, you usually start R in the directory that contains your bam files and then do something like

library(Rsamtools)
bfl <- BamFileList(dir(".", "bam$"), yieldsize = 2e6)

Which is a shorter way of doing something like this

## look for all files in the current directory that end with 'bam'
bamfiles <- dir(".", "bam$")

## load all those files into a BamFileList
bfl <- BamFileList(bamfiles, yieldsize = 2e6)

And then you would proceed with the rest of the RNA-Seq workflow.

Hi, 
It has been days that I'm struggling to make this line working .. but I can't do by myself.

this is what I get

> library( "GenomicFeatures" )
> library(TxDb.Hsapiens.UCSC.hg38.knownGene)
> tx_by_exon <- exonsBy(TxDb.Hsapiens,UCSC.hg38.knownGene)
Error in exonsBy(TxDb.Hsapiens, UCSC.hg38.knownGene) : 
  object 'TxDb.Hsapiens' not found 

exonBy is under GenomicFeature but it gives me errors, can you please help me with that?
 

Or maybe I can use a different way for counting reads in genes and make the matrice 

I will appreciate a lot 

thank you 

I messed up the topic, I changed something from the first posts. 
I will summarize here all my codes:


I created fist the bam files list:

list_bam <- lapply ( c("SRR1039508_subset.bam", "SRR1039512_subset.bam",

                       "SRR1039516_subset.bam","SRR1039520_subset.bam","SRR1039509_subset.bam",

                       "SRR1039513_subset.bam" , "SRR1039517_subset.bam","SRR1039521_subset.bam"  )   , scanBam )

I generated the full paths to the files I want to perform the counting operation on:

bamFiles <- file.path("/Users/patriziopanelli/Documents/BamFilesTest",sampleTable$fileName )

bamFiles

Launch this code by protocol

seqinfo( BamFile( bamFiles[1] ) )

I created a GRange list

txdb <-TxDb.Hsapiens.UCSC.hg38.knownGene

grl <- exonsBy(txdb, by="gene")

grl

And now I'm stuck here...

tx_by_exon <- exonsBy(TxDb.Hsapiens.UCSC.hg38.knownGene)

library( "GenomicAlignments" )

se <- summarizeOverlaps( exonsByGene, BamFileList( bamFiles ), mode="Union",

                        singleEnd=FALSE, ignore.strand=TRUE, fragments=TRUE )

I can assure that it ain't been easy to reach this point, yes I m new to Rstudio and RNAseq analysis but to me every time I go further each step it's a great satisfaction and I don't want to get lost in tons or codes of R ..I'm trying to learn it by using it. 

I hope this post can clarify the work that I m doing ..or if there is something wrong, please tell me. My goal for now is to create the count matrice 

Thank you 

The simplest and fastest Bioconductor way to get gene counts from aligned BAM files is to use featureCounts(). For example

files <- c("SRR1039508_subset.bam", "SRR1039512_subset.bam",
           "SRR1039516_subset.bam", "SRR1039520_subset.bam",
           "SRR1039509_subset.bam", "SRR1039513_subset.bam",
           "SRR1039517_subset.bam", "SRR1039521_subset.bam")
fc <- featureCounts(files, annot.inbuilt="hg38")

Then the matrix of counts is found in fc$counts.