How do I read a BAM file？

[BeyondMyPast228]

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 my own BAM file for analysis? I tried a few, as shown below: bamfile <- readBamFile("/home/vip1/atac/align/ms3468-2.last.bam") bamfile.labels <- "ms3468-2.last" estimateLibComplexity(readsDupFreq(bamfile)) The first two lines of code worked fine, but the third line gave me an error. The error is : Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'testPairedEndBam' for signature '"GAlignments"

I sincerely hope to get your kind reply.

[jianhong]

Hi, Thank you for reporting this bug. Please try estimateLibComplexity(readsDupFreq( "/home/vip1/atac/align/ms3468-2.last.bam"**)) in current release version. I will try to fix this soon.

On Tue, Nov 3, 2020 at 6:16 AM BeyondMyPast228 [email protected] wrote:

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 my own BAM file for analysis? I tried a few, as shown below:

bamfile <- readBamFile("/home/vip1/atac/align/ms3468-2.last.bam") bamfile.labels <- "ms3468-2.last" estimateLibComplexity(readsDupFreq(bamfile)) The first two lines of code worked fine, but the third line gave me an error. The error is : Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'testPairedEndBam' for signature '"GAlignments"

I sincerely hope to get your kind reply.

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