Can deduplicate_bismark (the component of bismark) script distinguish single-end/paired-end BAM/SAM Bismark files directly ?

[changchuanjun]

@FelixKrueger,
In deduplicate_bismark script instruction part, It persents can detect single-end/paired-end BAM/SAM Bismark files automatically.

But when I ran this script using paired-end BAM/SAM Bismark files,It detect it a single-end BAM/SAM Bismark file. It is very weird.

So I am confused that whether deduplicate_bismark (the component of bismark) script distinguish single-end/paired-end BAM/SAM Bismark files directly.Or when I ran deduplicate_bismark script with the -p parameter?

[FelixKrueger]

Which version of deduplicate_bismark are you using?

[changchuanjun]

@FelixKrueger
Deduplicator Version: v0.24.2

[changchuanjun]

@FelixKrueger
Deduplicator Version: v0.24.2

[FelixKrueger]

Ok thanks. It appears that the top message should probably just say Bismark output files, and lose the '--single-end'. I'll have that changed.

The last line of the screen-shot above says: "Treating file as paired-end file". So that is good, this is the important bit.

[changchuanjun]

OK.
So Can deduplicate_bismark script distinguish single-end/paired-end BAM/SAM Bismark files directly?
Or when I ran deduplicate_bismark script with the parameter --paired ?

[FelixKrueger]

either is fine. The distinction is that the auto-detection work on a per file basis, whereas -p works for all files supplied.