Closed changchuanjun closed 4 months ago
Which version of deduplicate_bismark
are you using?
@FelixKrueger
Deduplicator Version: v0.24.2
@FelixKrueger
Deduplicator Version: v0.24.2
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.
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 ?
either is fine. The distinction is that the auto-detection work on a per file basis, whereas -p
works for all files supplied.
@FelixKrueger, In deduplicate_bismark script instruction part, It persents can detect single-end/paired-end BAM/SAM Bismark files automatically.![image](https://github.com/FelixKrueger/Bismark/assets/155738984/986477a1-89af-4b2c-bf2a-56c0a491addb)
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.![image](https://github.com/FelixKrueger/Bismark/assets/155738984/a4bbb92d-5bbd-4315-8ddc-8cbfde065225)
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?