I just noticed that you have a typo in the following code.
bamTop100 <- scanBam(BamFile(bamfilde, yieldSize = 100),
param = ScanBamParam(tag=possibleTag))[]$tag
It should be bamfile instead of bamfilde.
bamTop100 <- scanBam(BamFile(bamfile, yieldSize ...
... Could you please share your session information with us? The most recent release of ATACseqQC is 1.8.1 (https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html). Thanks!
... Thanks Jim for identifying the issue!
Shuang, could you please use the most recent release ATACseqQC 1.8.1 (Bioc 3.9 and R 3.6) at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html? Thanks!
It seem that your library contains a lot of mitochondria DNA, which is a waste of reads. For your future reference, it is more efficient to deplete mitochondria DNA when constructing the ATAC-seq sequencing library.
I am wondering what the fragment size distribution looks like (ATACseqQC::fr ...
In MCCB of University of Massachusetts Medical School, we have developed a core team of accomplished computational biologists who work side-by-side with bench scientists to evaluate, select and develop algorithms and software pipelines to analyze, annotate, visualize and integrate various ...
... A post-doctoral position in bioinformatics and computational biology is available in Prof. Julie Zhu's group in the Department of Molecular, Cell and Cancer Biology at the University of Massachusetts Medical School, located in Worcester MA.
Research projects in Dr. Zhu's group include (1) developme ...
Please download the newest version of CRISPRseek (Version: 1.25.2). To find paired gRNAs with PAM face inwards towards each other, please set paired.orientation = "PAMin".
To obtain the most recent dev version of CRISPRseek, please type the following command in a terminal.
git clone git@git ...
Thanks for posting the question! I will add the functionality and let you know when it is done.