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 notifications@github.com 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’

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[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 notifications@github.com 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

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[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 notifications@github.com 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 +---------------------------------------------------------------------------------------

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