How to prepare sampleTable.tsv ?

[shaohuaihan]

sampleTable <- fread(system.file(
"extdata", "sampleTable.tsv", package="FRASER", mustWork=TRUE))
head(sampleTable)

sampleID bamFile group gene pairedEnd

1: sample1 extdata/bam/sample1.bam 1 TIMMDC1 TRUE

2: sample2 extdata/bam/sample2.bam 3 CLPP TRUE

3: sample3 extdata/bam/sample3.bam 2 MCOLN1 TRUE

In you example, If I have 1000 samples, can only prepare a file for repetitive genes, but can't specify a GTF file as input ?

Thank you !

[AtaJadidAhari]

Hi @shaohuaihan, the gene column here is later used to limit the set of genes in p-value calculation (more info here). You don't need to have this column in your dataset if you don't want to restrict the p-value calculation. A gene annotation file (TxDb.Hsapiens.UCSC) will be later loaded to annotate the junctions/genes. You can check the vignette section Quick guide to FRASER for more details.
Just as a side note, if you have around 1000 samples, I strongly recommend you to use DROP to run FRASER.