Phased SNP.vcf file

[ruqianl]

Hi @HeQSun ,

Very impressive pipeline!

I'm interested in the crossover identification step for the scCNV-sequenced nuclei. I have downloaded the aligned bam for the two 10xCNV libraries (thanks for sharing the dataset).

4279_A_run615_cellranger_possorted_bam.bam 4279_A_run619_cellranger_possorted_bam.bam 4279_B_run617_cellranger_possorted_bam.bam 4350_A_run626_cellranger_possorted_bam.bam
4279_A_run617_cellranger_possorted_bam.bam 4279_B_run615_cellranger_possorted_bam.bam 4279_B_run619_cellranger_possorted_bam.bam 4350_B_run626_cellranger_possorted_bam.bam

And I'm wondering if you could share the informative SNP markers, i.e SNP.vcf file or could you point me to it if you already have ?

Many thanks,
Ruqian

[HeQSun]

Hi @HeQSun ,

Very impressive pipeline!

I'm interested in the crossover identification step for the scCNV-sequenced nuclei. I have downloaded the aligned bam for the two 10xCNV libraries (thanks for sharing the dataset).

4279_A_run615_cellranger_possorted_bam.bam 4279_A_run619_cellranger_possorted_bam.bam 4279_B_run617_cellranger_possorted_bam.bam 4350_A_run626_cellranger_possorted_bam.bam
4279_A_run617_cellranger_possorted_bam.bam 4279_B_run615_cellranger_possorted_bam.bam 4279_B_run619_cellranger_possorted_bam.bam 4350_B_run626_cellranger_possorted_bam.bam

And I'm wondering if you could share the informative SNP markers, i.e SNP.vcf file or could you point me to it if you already have ?

Many thanks,
Ruqian

Hi Ruqian,

the bam files cannot be directly used for your purpose (as reads were not aligned to the original genome).

You should (pls find details in pipeline):

1. convert the bam into fastq files
2. extract read sets for individual nuclei and those with barcodes in the attached file below were found to be haploid
3. align each set of reads (=nuclei) independently to one of our haplotype genome assembly (at NCBI database)
4. align all pooled fastq reads to the same assembly to define snp markers.
5. predict COs using TIGER pipeline (using snp markers at step 4 and alignment info at step 3).

Best,
Hequan

445_barcode.txt

[ruqianl]

Hi @HeQSun ,
Very impressive pipeline!
I'm interested in the crossover identification step for the scCNV-sequenced nuclei. I have downloaded the aligned bam for the two 10xCNV libraries (thanks for sharing the dataset).
4279_A_run615_cellranger_possorted_bam.bam 4279_A_run619_cellranger_possorted_bam.bam 4279_B_run617_cellranger_possorted_bam.bam 4350_A_run626_cellranger_possorted_bam.bam
4279_A_run617_cellranger_possorted_bam.bam 4279_B_run615_cellranger_possorted_bam.bam 4279_B_run619_cellranger_possorted_bam.bam 4350_B_run626_cellranger_possorted_bam.bam
And I'm wondering if you could share the informative SNP markers, i.e SNP.vcf file or could you point me to it if you already have ?
Many thanks,
Ruqian

Hi Ruqian,

the bam files cannot be directly used for your purpose (as reads were not aligned to the original genome).

You should (pls find details in pipeline):

1. convert the bam into fastq files
2. extract read sets for individual nuclei and those with barcodes in the attached file below were found to be haploid
3. align each set of reads (=nuclei) independently to one of our haplotype genome assembly (at NCBI database)
4. align all pooled fastq reads to the same assembly to define snp markers.
5. predict COs using TIGER pipeline (using snp markers at step 4 and alignment info at step 3).

Best,
Hequan

445_barcode.txt

Thanks!
I'm going to have a go with your suggested steps.

Best,
Ruqian