jianhong / ATACseqQC

ATAC-seq Quality Control

https://jianhong.github.io/ATACseqQC/articles/ATACseqQC.html

jianhong/ATACseqQC Issues

Optimizing Time and Memory Usage for Large BAM Files
Updated 8 months ago6
Error in TSSEscore calculation
Closed a year ago15
should the original bam be deduped and chrM deleted for the analysis of fragSizeDist()?
Closed a year ago2
Interpreting the outputs of the function TSSEscore() comparing to the reference from ENCODE
Updated 2 years ago5
Read the shifted bam and continue the QC analysis
Updated 2 years ago7
phastCons100way.UCSC.hg19 equivalent for mm10 ?
Updated 2 years ago7
Error: subscript contains invalid names for splitGAlignmentsByCut() function
Closed 2 years ago8
adjusting readBamFile output for plotCorrelation
Updated 2 years ago4
Question about the read filtering by bamQC
Updated 2 years ago1
Question about bamQC
Updated 2 years ago1
Strange TSS Enrichment Result
Updated 2 years ago1
different TSS.filter values affect the signals showing on the heatmap
Updated 2 years ago1
Output bam files become smaller after shiftGAlignmentsList
Updated 2 years ago4
NA values in sigs makes heatmap not completed
Closed 2 years ago4
What does the x axis mean for Nucleosome Free Regions (NFR) score plot?
Closed 2 years ago3
Error on running splitBam
Closed 3 years ago13
Processing multiple bam files at once
Closed 3 years ago2
splitBam fragment sizes for nucleosome-free DNA
Updated 3 years ago2
splitGAlignmentsByCut Error in value[[3L]](cond) : 'mergeBam' 'destination' exists, 'overwrite' is FALSE destination: splitBam/NucleosomeFree.bam
Updated 3 years ago8
splitGAlignmentsByCut 'mergeBam' error
Closed 4 years ago7
splitBam return a asBam error
Updated 4 years ago3
Problem with shiftGAlignmentsList()
Updated 4 years ago2
How do I read a BAM file？
Updated 4 years ago1
shiftGAlignmentsList() error
Updated 4 years ago1
CIGAR and query sequence are of different length, as.Bam truncated input
Closed 4 years ago
plot correlation is not symmetric
Closed 4 years ago1
estimateLibComplexity error
Updated 4 years ago
error in factorFootprints function
Closed 4 years ago1
inconsistencies between the package code and user guide
Closed 4 years ago1
factorFootprints 'seqnames' issue
Updated 4 years ago5
factorFootprints error on system.file("extdata", "GL1.bam",package="ATACseqQC")
Updated 4 years ago2
Pls help with the error... I am using hg38
Updated 4 years ago1
Remove interactive() in readBamFile.R
Updated 4 years ago
Question about readBamFile function
Updated 4 years ago20
shiftGAlignmentsList after samtools fixmate error
Closed 4 years ago14
How to normalize cut-site probability between samples
Updated 5 years ago
error when install ATACseqQC
Updated 5 years ago7
error running factorFootprints -- evaluations nested too deeply
Updated 5 years ago
shiftGAlignmentsList Error
Updated 5 years ago3
treated as unmapped - splitGAlignmentsByCut
Updated 5 years ago2
TF footprint figure
Updated 5 years ago
How the cut-site probability is calculated?
Updated 5 years ago1
shiftGAlignmentsList time
Updated 6 years ago4
Issue: loading bam file using readBamFile uses huge amount of memory causing crashes
Updated 6 years ago14
no "estimateLibComplexity"
Updated 6 years ago3
Adjust the read start sites of mouse data
Updated 6 years ago1
single reads and distal regions
Closed 6 years ago2
Error : object 'gscores' is not exported by 'namespace:GenomicScores'
Closed 6 years ago1
Error when ATACseqQC load preseqR function ds.mincount.bootstrap
Closed 6 years ago1
Request: Supporting BamFile and BamFileList as `bamFiles` arg
Updated 6 years ago3