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problem in creating Arrow Files from Bam file

Open zara03 opened this issue 1 year ago • 1 comments

Hi I am very new to ArchR . I have downloaded a public dataset and i indexed the fastq with hg19 as they mentioned in paper.This created sam file, which i converted into bam and then indexed the bam.the indexing created 2 files SRR7784432_aligned.bam and SRR7784432_aligned.bam.bai.

Code: bowtie2 -x hg19_index -U /home/saz22/snATAC_GSE119453_hg19_Data/SRR7784432.fastq -S SRR7784432_aligned.sam

samtools view -bS SRR7784432_aligned.sam | samtools sort -o SRR7784432_aligned.bam

samtools index SRR7784432_aligned.bam

No i am trying to read SRR7784432_aligned.bam as input to create arrow file and it gives me error first it was input is not indexed and now this is error i am facing.

ArrowFiles <- createArrowFiles( inputFiles = "/home/zs/SRR7784432_aligned.bam",
sampleNames = "Sample_SRR7784432",
geneAnnotation = getGeneAnnotation("hg19"),
genomeAnnotation = getGenomeAnnotation("hg19"),
minTSS = 4,
minFrags = 1000,
addTileMat = TRUE,
addGeneScoreMat = TRUE) Error in .validInput(input = ArchRProj, name = "ArchRProj", valid = c("ArchRProject", : Input value for 'ArchRProj' is not a null,archrproject, (ArchRProj = character) please supply valid input!

Any suggestion will be of great help.

zara03 avatar Oct 22 '24 21:10 zara03