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ncbi / BAMscale

BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.
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strand-specific definition #19

Open mmpust opened 1 year ago

mmpust commented 1 year ago

Hi,

is endseq: strand-specific coverages in this context referring to the strand specificity based on the underlying DNA reference or based on sense/antisense RNA transcription for strand-specific RNA libraries?

Thanks!

pongorlorinc commented 1 year ago

Hi,

To my understanding the END-seq is sequenced in a strand specific manner, so the strand information can be retrieved by the alignment orientation, which is used by BAMscale.

Hope this helps!

Best wishes, Lorinc

mmpust commented 1 year ago

Thanks for your quick reply! Can you explain this a bit more? Because my library is strand-specific. Thus, I have sense and antisense transcription in a bacterial cell. But both DNA strands in a bacterial genome (positive and negative strand) can act as template for sense and antisense transcription. So, is BAMscale referring to the positive/negative DNA strand/template or sense/antisense transcription of a gene? Thanks!