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smarco / gem3-mapper

GEM-Mapper v3
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questions about gem-mapper #22

Closed biozzq closed 3 years ago

biozzq commented 3 years ago

Dear @smarco

I think this question ( https://github.com/smarco/gem3-mapper/issues/21) should be related to gem-mapper, I just want to know how to set the --underconversion-sequence, --overconversion-sequence, and --control-sequence optimally.

 [Bisulfite and Hi-C Alignment]
      --bisulfite-conversion 'inferred-C2T-G2A','inferred-G2A-C2T','C2T','G2A','non-stranded' (default=inferred-C2T-G2A)
      --underconversion-sequence <sequence name> (default=NC_001416.1)
      --overconversion-sequence <sequence name> (default=NC_001604.1)
      --control-sequence <sequence name> (default=NC_001422.1)

Best wishes, Zheng zhuqing

heathsc commented 3 years ago

Dear Zheng,

The questions relate more to the functions of the mapper within the gemBS pipeline than to the basic mapping functions themselves.

The conversion and control sequences should be set to the names of the sequences that were added into the sequence library to act as controls. If these are not set correctly then gemBS will not be able to estimate the conversion rates, but it will not affect the mapping process. For Illumina sequencing the control sequence is typically Phi-X (NC_001422.1), and for WGBS sequencing the undeconversion control (if used) is often Phage lambda (NC_001416.1). There is no widely used over conversion sequence as far as I know. Note that the conversion sequences should be included in the reference FASTA file used to build the GEM mapping index.

The --bisulfite-conversion option allows different sequencing library characteristics.

Stranded libraries:

inferred-C2T-G2A Read 1 is C depleted, read 2 is G depleted (most common configuration) inferred-G2A-C2T Read 1 is G depleted, read 2 is C depleted C2T All reads are C depleted G2A All reads are G depleted

Non stranded libraries

non-stranded Each read pair can either be C2T-G2A or G2A-C2T independently of the other reads

Simon

On Tue, Jan 12, 2021 at 8:26 AM biozzq notifications@github.com wrote:

Dear @smarco https://github.com/smarco

I think this question ( #21 https://github.com/smarco/gem3-mapper/issues/21) should be related to gem-mapper, I just want to know how to set the --underconversion-sequence, --overconversion-sequence, and --control-sequence optimally.

[Bisulfite and Hi-C Alignment] --bisulfite-conversion 'inferred-C2T-G2A','inferred-G2A-C2T','C2T','G2A','non-stranded' (default=inferred-C2T-G2A) --underconversion-sequence (default=NC_001416.1) --overconversion-sequence (default=NC_001604.1) --control-sequence (default=NC_001422.1)

Best wishes, Zheng zhuqing

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biozzq commented 3 years ago

Dear Simon,

Thank you for your explanation.

Best wishes, Zheng zhuqing