about the detectbeadsubstitutionerrors module!

[10KGenomics]

Dear sir

Hello! Please ask questions about the detectbeadsubstitutionerrors module! Got report Txt, the results are as follows:

What the Intended_ size、neighbor_size mean? Is this the number of overwritten reads of the cell barcode? If the repaired column is true, correct the barcode base and enter the next analysis.

[jamesnemesh]

Hi, The intended size is the number of UMIs for what we believe is the original error free cell barcode. The the neighbor size is the number of UMIs in a related cell barcode that we think should be merged. Repaired=T means that the two sets of UMIs will be merged into the intended barcode. Your barcodes look very different from the standard dropseq or 10x reaction - it looks like you have a cell barcode, UMI, and polyA tail on every barcode. Are you running a very different protocol and you’re confident in retaining all of those bases?

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-Jim

On May 4, 2022, at 5:06 AM, caijingtao1993 ***@***.***> wrote: Dear sir Hello! Please ask questions about the detectbeadsubstitutionerrors module! Got report Txt, the results are as follows: <https://user-images.githubusercontent.com/67781404/166652335-22bd1dfd-d5dc-484e-bfc4-4f899a6b752b.png> What the Intended_ size、neighbor_size mean? Is this the number of overwritten reads of the cell barcode? If the repaired column is true, correct the barcode base and enter the next analysis. — Reply to this email directly, view it on GitHub <#304>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABCZXJ2EAK6U5G52SPTYPKDVII423ANCNFSM5VBKCO7Q>. You are receiving this because you are subscribed to this thread.

[10KGenomics]

Hi, The intended size is the number of UMIs for what we believe is the original error free cell barcode. The the neighbor size is the number of UMIs in a related cell barcode that we think should be merged. Repaired=T means that the two sets of UMIs will be merged into the intended barcode. Your barcodes look very different from the standard dropseq or 10x reaction - it looks like you have a cell barcode, UMI, and polyA tail on every barcode. Are you running a very different protocol and you’re confident in retaining all of those bases?
…
-Jim
On May 4, 2022, at 5:06 AM, caijingtao1993 @.***> wrote: Dear sir Hello! Please ask questions about the detectbeadsubstitutionerrors module! Got report Txt, the results are as follows: https://user-images.githubusercontent.com/67781404/166652335-22bd1dfd-d5dc-484e-bfc4-4f899a6b752b.png What the Intended_ size、neighbor_size mean? Is this the number of overwritten reads of the cell barcode? If the repaired column is true, correct the barcode base and enter the next analysis. — Reply to this email directly, view it on GitHub <#304>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABCZXJ2EAK6U5G52SPTYPKDVII423ANCNFSM5VBKCO7Q. You are receiving this because you are subscribed to this thread.

yes. Thank you for your reply, sir. I default both the link sequence and the ployT sequence as part of the barcode, so the barcode is long. What is the basis for determining repaired = t? In addition, EDIT_DISTANCE parameter defaults to 1. If it is set to 2, does it mean that there are two different bases in the barcode sequence and will it be corrected?