ATACseqQC

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splitBam return a asBam error

3

Hi, I have a problem with just one bam file for splitBam step. My script do splitBam step for each chromosome of each bamfiles in bamfile list. ``` bamfile

jupollet

Problem with shiftGAlignmentsList()

2

Thanks for your package! I'm going to generate a TSSE score plot for an bulk ATAC-seq data and I use code below: possibleTag

jingyu0602

How do I read a BAM file？

1

Hi， Thanks for developing this user-friendly tool. This is my first contact with **ATACseqQC**. In your tutorial, the BAM file is built into the R package. How can I use...

BeyondMyPast228

shiftGAlignmentsList() error

1

Hello, I've been running the function and see following error many times: [bam_translate] RG tag "1" on read "K00180:164:HCG3YBBXX:2:1207:28057:2879" encountered with no corresponding entry in header, tag lost. Unknown tags...

hirokomatsui

Hi ATACseqQC team, thanks for your nice package for atac-seq quality control. I get an error while i am doing estimateLibComplexity(readsDupFreq("test.bam")) it gives me the following error: ********************************************************************************************************************* Error in...

noorisotoudeh

factorFootprints 'seqnames' issue

5

Hi @jianhong I am having an issue with the factorFootprints coding. I can run everything up to this point fine, but when I try to run this through, I get...

mmilevskiy

factorFootprints error on system.file("extdata", "GL1.bam",package="ATACseqQC")

2

Hi, when I follow the examples to run factorFootprints for ATACseqQC v1.12.0 on GL1.bam file from the ATACseqQC manual document or from the ATACseqQC guide, I am getting segfault. Any...

tinavisnovska

Pls help with the error... I am using hg38

1

objs

hjack123

https://github.com/jianhong/ATACseqQC/blob/2996d20e9b39825b38d580b2c38636199975d29e/R/readBamFile.R#L47 The `interactive()` is anti-human and redundant. This is in particular annoying in Rstudio server. I highly suggest removing this condition.

Puriney

Question about readBamFile function

20

Hi, First thanks to build this package it is very interesting tool. So I'm trying to integrate your package in my ATACseq pipeline. But I have some issue. In fact,...

El-Castor