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Can deduplicate_bismark (the component of bismark) script distinguish single-end/paired-end BAM/SAM Bismark files directly ? #659
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Which version of |
@FelixKrueger |
1 similar comment
@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. |
OK. |
either is fine. The distinction is that the auto-detection work on a per file basis, whereas |
@FelixKrueger,
![image](https://private-user-images.githubusercontent.com/155738984/309277913-986477a1-89af-4b2c-bf2a-56c0a491addb.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjYxNjczODksIm5iZiI6MTcyNjE2NzA4OSwicGF0aCI6Ii8xNTU3Mzg5ODQvMzA5Mjc3OTEzLTk4NjQ3N2ExLTg5YWYtNGIyYy1iZjJhLTU2YzBhNDkxYWRkYi5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwOTEyJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDkxMlQxODUxMjlaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT0wMDlhOTNjN2FhNTBjMDVmMjQ5YmUyMDFiZDkyOGRmZmRlYTFlNjQ5ODBjNmI4OTUwNWE1NjI0OGU0ZTAxMGRmJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.4zNZuKrUnje99c05cQ_EED4s7AblPAIoXRqu-8yt0KY)
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.
![image](https://private-user-images.githubusercontent.com/155738984/309280503-a4bbb92d-5bbd-4315-8ddc-8cbfde065225.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjYxNjczODksIm5iZiI6MTcyNjE2NzA4OSwicGF0aCI6Ii8xNTU3Mzg5ODQvMzA5MjgwNTAzLWE0YmJiOTJkLTViYmQtNDMxNS04ZGRjLThjYmZkZTA2NTIyNS5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwOTEyJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDkxMlQxODUxMjlaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT04ZjgwNGU4YzE2ZTU1NjE4ZTM4MTg3YTUxYmFiMzkxYTg5Njg4MzNmYWJjODg1OGYxYTFjMTk2M2FkYWIyNmY2JlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.v0cYu1d2Oa5q7x4d2tEBEdZmiYRhYsvRPRCZ3wqIuRs)
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?
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