ATACseqQC

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Read the shifted bam and continue the QC analysis

7

Hello Jianhong, Thanks for your excellent work! My bam file is so big that it costs a lot of resources during the running. In order to reduce the time consumption,...

XiaoyuZhan520

phastCons100way.UCSC.hg19 equivalent for mm10 ?

7

Hi, I work with mouse genome (mm10) and i don't find any phastCons100way.UCSC.hg19 equivalent for mm10 to do the "Split reads" part of bioconductor tutorial. Sorry for my bad english....

Just08

adjusting readBamFile output for plotCorrelation

4

Hi, (in ATACseqQC 1.12.0) the example of using plotCorrelation that is written in the ATACseqQC guide works out of the box only when asMates and bigFile parameters are FALSE in...

tinavisnovska

Question about the read filtering by bamQC

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Hi Jianhong, Besides the reads with low alignment scores, the reads derived from mitochondrial DNA and the PCR/optical duplicates, are there any other filters applied by bamQC? What are the...

etiennedanis

Question about bamQC

1

Hi Jianhong, Thank you again so much for creating ATACseqQC! To get the report of all the QC metrics with bamQC, it looks like I should use: **bamQC(bamFile, outPath =...

etiennedanis

Strange TSS Enrichment Result

1

Hello, I am getting a very strange result for the plot of TSS enrichment (see attached image). I have tried other packages that do QC for ATACseq and they gave...

astarr97

different TSS.filter values affect the signals showing on the heatmap

1

Hello @jianhong Thanks for pushing the patch fixing the NA problem. I can generate the complete heatmap now. However, the red signals of heatmap are still partially shown on the...

hyjforesight

Output bam files become smaller after shiftGAlignmentsList

4

Hi, Thanks for developing this user-friendly tool for ATAC-seq. I found some problems after running shiftGAlignmentsList, and the output BAM file is about half the size of the input file....

Rui-Jing

splitBam fragment sizes for nucleosome-free DNA

2

Hi, I'm using your package and have a general question regarding the sizes in which BAM file is split with splitBam to generate nucleosome-free, mononucleosome... fragments. I see that the...

rauldiul

splitGAlignmentsByCut Error in value[[3L]](cond) : 'mergeBam' 'destination' exists, 'overwrite' is FALSE destination: splitBam/NucleosomeFree.bam

8

Hi, I know this is an old error, but I have the same problem. I'm using ATACseqQC 1.8.5 and R 3.6.1, and I get the same error when I run...

rafet2005