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Lordhooze avatar Lordhooze commented on August 15, 2024

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

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alauring avatar alauring commented on August 15, 2024

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Lordhooze avatar Lordhooze commented on August 15, 2024

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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alauring avatar alauring commented on August 15, 2024

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Lordhooze avatar Lordhooze commented on August 15, 2024

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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alauring avatar alauring commented on August 15, 2024

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