Unmatching d_germline_alignment indexes to the length of the d segment in BCR sequences #1532
-
|
I used the exportAIRR command to annotate BCR sequences obtained from different tissues of a mouse. I have uploaded a screenshot of the some reads. for example in this case, the sequence was annotated with IDHD5-8 d segment which has a length of 10 nuceltodies: "GAGTACCTAC", however in the output of MIXCR the indexes are d_germline_start: 31 and d_germline_end: 39. how can the indexes be larger than the length of the d segment ? 
|
Beta Was this translation helpful? Give feedback.
Replies: 3 comments 4 replies
-
|
Hi, |
Beta Was this translation helpful? Give feedback.
-
|
Hey, Does this apply also for the V germline end, the J germline start and end? sequence_id read.5 |
Beta Was this translation helpful? Give feedback.
-
|
yes, V end and J start follow the same logic due to the P segment reference |
Beta Was this translation helpful? Give feedback.
-
|
thanks for the fast reply,
I am trying to use the output data of MIXCR to add a
sequence_germline_d_mask column to the data using another tool (dowser
library in R).
I understand that the indexing of the d segment is not the conventional of
the AIRR format and this leads of problem when using other tools.
Is there an easy way to convert the indexing of the d segment that includes
the identification of the palindrome sequence, into indexing of only the d
segment ?
Is the palindrome sequence always the same length of the d segment ? In
such a case I can simply reduce from the start / end index the length of
the d segment to the indexing of the d segment?
thanks a head for the help,
bar avidov
…On Fri, Feb 9, 2024 at 11:59 PM mizraelson ***@***.***> wrote:
Hi,
MiXCR incorporates P segment detection, which means that the reference
sequence for each gene includes parts accounting for the P segment.
Specifically, for the D gene, this involves an inverted sequence both
before and after the actual D gene to accommodate potential P nucleotides.
For instance, the IGHD5-8 gene is 29 nucleotides long
<https://vdj.online/library/gene/10090:IGHD5-8>. In the reference, the
first 29 nucleotides represent the P segment before the D gene, followed by
29 nucleotides of the D gene itself, and then another 29 nucleotides for
the P segment after the D gene. Therefore, a position marked as '31'
indicates the 2nd nucleotide of the D gene. Conversely, a position marked
as '24' would imply the presence of 6 P-nucleotides before the start of the
D gene.
—
Reply to this email directly, view it on GitHub
<#1532 (comment)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/A4CRMWMWPHABH4JIZJJCEHDYS2L3NAVCNFSM6AAAAABC75SPUWVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4DIMRTGY4DA>
.
You are receiving this because you authored the thread.Message ID:
***@***.***>
|
Beta Was this translation helpful? Give feedback.
-
|
Yes, the palindrome is always the same length as the D gene itself. |
Beta Was this translation helpful? Give feedback.
-
|
Is there a way to convert the indexes into the indexes often used in the
AIRR format which include only the indexes of the d segment germ line part
without the palinedrom ?
…On Sun, Feb 11, 2024 at 11:26 AM mizraelson ***@***.***> wrote:
Yes, the palindrome is always the same length as the D gene itself.
—
Reply to this email directly, view it on GitHub
<#1532 (reply in thread)>,
or unsubscribe
<https://github.com/notifications/unsubscribe-auth/A4CRMWNSTGUK6IYCKPVS5ALYTCFDLAVCNFSM6AAAAABC75SPUWVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4DIMZRG42DE>
.
You are receiving this because you authored the thread.Message ID:
***@***.***>
|
Beta Was this translation helpful? Give feedback.
-
|
Currently we do not have such conversion, but will add it in the future. |
Beta Was this translation helpful? Give feedback.
Hi,
MiXCR incorporates P segment detection, which means that the reference sequence for each gene includes parts accounting for the P segment. Specifically, for the D gene, this involves an inverted sequence both before and after the actual D gene to accommodate potential P nucleotides. For instance, the IGHD5-8 gene is 29 nucleotides long. In the reference, the first 29 nucleotides represent the P segment before the D gene, followed by 29 nucleotides of the D gene itself, and then another 29 nucleotides for the P segment after the D gene. Therefore, a position marked as '31' indicates the 2nd nucleotide of the D gene. Conversely, a position marked as '24' would imply the presence of 6 P-…