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Question - about the result of kept_barcodes_binned.txt.BCUMIstats.txt #381
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Hi, So for this particular 11bp pattern "ATTGCGCAATG" which corresponds to the Smart-seq3 TSO, our pipeline is hardcoded to only take it when it is present in the start of the read! |
Thanks a lot for your reply. Have a nice day! |
What does "hardcoded" mean? How can I solve this problem? |
Hi,
![1](https://private-user-images.githubusercontent.com/109192357/284229951-5d0e72a3-8274-4503-ba43-f116b7c3719f.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjE0NDI4NDUsIm5iZiI6MTcyMTQ0MjU0NSwicGF0aCI6Ii8xMDkxOTIzNTcvMjg0MjI5OTUxLTVkMGU3MmEzLTgyNzQtNDUwMy1iYTQzLWYxMTZiN2MzNzE5Zi5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNzIwJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDcyMFQwMjI5MDVaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT1kY2U3ZTEyYTQzZTdkNTA0MzU3OTY4YTRmOGVjYzBhYjViODI4Y2I4NzIwZDMxZmNhMDMxMzE0ZTc5OTY3ZGYzJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.6tVjYGQXbLWA9BVofi7e7ciHxGztf0cF_r9Z6X40kX4)
Below is my pm1kept_barcodes_binned.txt.BCUMIstats.txt result. I wanna know how the "nNontagged" and "nUMItag" columns comes.
then i chose the bc "AGATTGACTCACTAGGTGACAC" , and serch it in pm1.filtered.tagged.Aligned.toTranscriptome.out.bam, and i found that UB tag is null
![2](https://private-user-images.githubusercontent.com/109192357/284230632-85444797-4710-41ba-abdb-77b6774c9088.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjE0NDI4NDUsIm5iZiI6MTcyMTQ0MjU0NSwicGF0aCI6Ii8xMDkxOTIzNTcvMjg0MjMwNjMyLTg1NDQ0Nzk3LTQ3MTAtNDFiYS1hYmRiLTc3YjY3NzRjOTA4OC5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNzIwJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDcyMFQwMjI5MDVaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT04NTYwMzJjY2RlOTI2YTFjYjEzMTJjZDNkNzIzMWFlNWY3NTk5YjczNGEzOWViMjI1NmI5NzYyMTQ0YWViMGU1JlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9._ZzzK-_wRE8vnftW9Frvjjndnti9W37A6XMW0dOm4a4)
![5](https://private-user-images.githubusercontent.com/109192357/284232046-7c3af2b5-182c-446d-b877-f260b94cfe30.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjE0NDI4NDUsIm5iZiI6MTcyMTQ0MjU0NSwicGF0aCI6Ii8xMDkxOTIzNTcvMjg0MjMyMDQ2LTdjM2FmMmI1LTE4MmMtNDQ2ZC1iODc3LWYyNjBiOTRjZmUzMC5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNzIwJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDcyMFQwMjI5MDVaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT00MzU2MGIxMDAyNGE4ZTdjZjU1NWI0N2ZkYmRiMWNhZGYyODk3YzQ5NTRmNjA0MzQ1OWMxMmM2YmFkNTI1NjVjJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.S8iznFQBZ8VWZhTHkE6V-vSDixVXE9Blc0NY_Ijvw1I)
then I got its corresponding reads, and I found that my pattern setted on my yaml is not at the beginning of my reads, below is my reads
![3](https://private-user-images.githubusercontent.com/109192357/284231076-84236c5a-52d2-45db-bab0-7307fffd79e2.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjE0NDI4NDUsIm5iZiI6MTcyMTQ0MjU0NSwicGF0aCI6Ii8xMDkxOTIzNTcvMjg0MjMxMDc2LTg0MjM2YzVhLTUyZDItNDVkYi1iYWIwLTczMDdmZmZkNzllMi5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNzIwJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDcyMFQwMjI5MDVaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT00MzhmZDAwZDIyY2M5M2VkNGJmOTJhMjkwMTBmNDE1YjIxM2I2NWQ3NWZmM2I0Nzk1M2RlMzI3ODA4YjM2MmRkJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.jgkGvYCsdPeoqummAONtLCsQ6eCh4aSPvSkY15sE9Bg)
below is my yaml text
pm1-1.yaml.txt
so the "nNontagged" and "nUMItag" columns result just because of the pattern not at the beginning of my reads?
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