control.bam

[Lordhooze]

Dear sir,
We used the Illumina platform to determine the whole genome consensus sequence and to
identify intrahost single nucleotide variants for each patient-derived sample
we want to using DeepSNV to identified single nucleotide variants (SNV)
which relies on a clonal control to estimate the，local error rate within a given sequence context and to identify strand bias in base calling. The
clonal control was a library prepared in an identical fashion from 8 plasmids containing the
genome for the respective circulating reference strain and sequenced in the same flow cell to
control for batch effects
But we don't know anything about ‘control’
Can you help us figure out what ‘control’ is and how to use ‘control’

[Lordhooze]

chicken 1 --> chicken 2 --> chicken 3 --> chicken 4 --> chicken 5 --> chicken 6
H9N2 virus passages from chicken1 to chicken 6
we want to using DeepSNV to identified single nucleotide variants (SNV)
We used the Illumina platform to determine the whole genome consensus sequence and to
identify intrahost single nucleotide variants
will you tell us, what is the control and how to generate the control bam file

[alauring]

The control is a plasmid containing the sequence that is closely related to the one you are sequencing. This follows from Gerstung et al. Nature Communications, the original description of DeepSNV. In our case, we are sequencing influenza virus. So we had a set of plasmids that together contained the entire genome. The plasmid is clonal and serves as a control for sequencing error. See also McCrone and Lauring, Journal of Virology 2016. - Adam

…

On Mar 14, 2019, at 3:59 AM, Lordhooze ***@***.***> wrote: Dear sir, We used the Illumina platform to determine the whole genome consensus sequence and to identify intrahost single nucleotide variants for each patient-derived sample we want to using DeepSNV to identified single nucleotide variants (SNV) which relies on a clonal control to estimate the，local error rate within a given sequence context and to identify strand bias in base calling. The clonal control was a library prepared in an identical fashion from 8 plasmids containing the genome for the respective circulating reference strain and sequenced in the same flow cell to control for batch effects But we don't know anything about ‘control’ Can you help us figure out what ‘control’ is and how to use ‘control’ — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#15>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AKC-HAjXTb3FntrxOk8wjcOBrdGd_pw5ks5vWgFUgaJpZM4bzhKY>.

[Lordhooze]

Dear sir,
below is our design of experiment
+-------------------------------------------------------------------------------------
| original H9N2 virus --> chicken 1 --> chicken 2 --> chicken 3 --> chicken 4
| H9N2 virus passages from chicken1 to chicken 4;
| we sequence the original H9N2 virus and the virus isolated from chicken 1 to chicken 4 respectively
+---------------------------------------------------------------------------------------
we want to use original H9N2 virus as control. They are active virus ( not plasmid). We sequenced the nucletide using illumina platform.
we want to use H9N2 virus isolated in chicken1; chicken 2; chicken 3; chicken 4 as samples (PE150; illumina)
Is that ok?

Many thanks

[alauring]

Without a plasmid control, you cannot use this approach to variant calling as designed. Adam

…

Sent from my iPhone

On Mar 14, 2019, at 7:48 AM, Lordhooze ***@***.***> wrote: Dear sir, below is our design of experiment +------------------------------------------------------------------------------------- | original H9N2 virus --> chicken 1 --> chicken 2 --> chicken 3 --> chicken 4 | H9N2 virus passages from chicken1 to chicken 4; | we sequence the original H9N2 virus and the virus isolated from chicken 1 to chicken 4 respectively +--------------------------------------------------------------------------------------- we want to use original H9N2 virus as control. They are active virus ( not plasmid). We sequenced the nucletide using illumina platform. we want to use H9N2 virus isolated in chicken1; chicken 2; chicken 3; chicken 4 as samples (PE150; illumina) Is that ok? Many thanks — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[Lordhooze]

could you recommend a software that is suitable to our design of experiment.
a software suitable to analysis SNV
below is our design of experiment
+-------------------------------------------------------------------------------------
| original H9N2 virus --> chicken 1 --> chicken 2 --> chicken 3 --> chicken 4
| H9N2 virus passages from chicken1 to chicken 4;
| we sequence the original H9N2 virus and the virus isolated from chicken 1 to chicken 4 respectively
| platform: illumina PE150
+---------------------------------------------------------------------------------------

[alauring]

There are a large number of variant callers out there and described in literature. That’s all I can really say. Adam

…

Sent from my iPhone

On Mar 14, 2019, at 8:34 AM, Lordhooze ***@***.***> wrote: could you recommend a software that is suitable to our design of experiment. a software suitable to analysis SNV below is our design of experiment +------------------------------------------------------------------------------------- | original H9N2 virus --> chicken 1 --> chicken 2 --> chicken 3 --> chicken 4 | H9N2 virus passages from chicken1 to chicken 4; | we sequence the original H9N2 virus and the virus isolated from chicken 1 to chicken 4 respectively | platform: illumina PE150 +--------------------------------------------------------------------------------------- — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.