How do I read a BAM file？
BeyondMyPast228 opened this issue · comments
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.
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 ***@***.***> 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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Yours sincerely,
Jianhong Ou