ATACseqQC

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Adjust the read start sites of mouse data

1

Hi, I installed ATACseqQC to offset ATAC-seq aligning. The example code in the Guide is for human data. I downloaded BSgenome.Mmusculus.UCSC.mm9 but I'm struggling with another part. seqlev

vibook

Request: Supporting BamFile and BamFileList as `bamFiles` arg

3

Would you consider supporting _BamFile_ and _BamFileList_ objects (from the **Rsamtools** package), in addition to _character_ vectors, as the `bamFiles` argument to functions in this package? This actually almost works...

PeteHaitch

Optimizing Time and Memory Usage for Large BAM Files

6

Hi, I've been trying to use ATACseqQC for quality control of some plant BAM files (exceeding 100GB in size). However, I encountered difficulties when attempting to run it, even after...

FarzanehRah

Interpreting the outputs of the function TSSEscore() comparing to the reference from ENCODE

5

Hello, First of all, thank you for developing ATACseqQC. I am having troubles interpreting the outputs of the function TSSEscore(). I am using the TSSE score definition used in [ENCODE...

SergioRodLla

estimated library size of NucleosomeFree.bam is unexpectedly small

2

Hi, After shift and splitting bams according to fragment size, I see amongst all bam the largest bam is NulceosomeFree.bam which is expected. However, when I run estLibSize (from ChIPpeakAnno...

cparsania

splitGAlignmentsByCut returns empty .bam files

12

The function runs and creates the NucleosomeFree.bam, mononucleosome.bam, dinucleosome.bam, and trinucleosome.bam files, but these files only contain some header info. There are no actual alignment records. The only message I...

chklee30

how do I read my shifted bam ad an obj in splitGalignmentsByCut

7

Hi again, so I have created and indexed the shifted bam files as in the tutorial. ```R gal

sunta3iouxos

readBamFile with bigFile=TRUE still returns 0 GAlignmentsList

2

Hi there, Thank youf or this tool, but I am still facing the same issues as a lot of time ago. My ATACseqQC version is 1.22.0 I am on windows...

sunta3iouxos