CP086569.1 is the first released Telomere-To-Telomere (T2T) sequence of a complete Y chromosome from a male human cell line. It might be possible that it contains regions which are not included in the GRCh38 / hg38 official reference sequence that is normally used. In an experimental approach it might be possible that in those sections novel SNPs can be found.

YSEQ offers a FASTQ mapping service to the CP086569.1 experimental reference sequence. The output is a BAM file of the Y chromosome and various VCF files with known and unknown variants. A further interpretation of the experimental results can't currently be given by YSEQ and this needs to be done by the customer himself. Therefore we only recommend to purchase this FASTQ Mapping to CP086569.1 service if you know how to handle BAM files and VCF files by yourself. Also we can't accept novel SNP submissions for positions on the CP086569.1 experimental reference sequence at this time because the database infrastructure for CP086569.1 SNPs is not yet established.

Is the CP086569.1 reference better than hg38?

In most cases not. It contains significantly more single base errors than the hg38 reference and the assembly structure is not clearly proven.
However it may be useful for samples in haplogroup J, and specifically J1, since it represents a Y chromosome that is closer related than the hg38 sequence which is known to represent R1b. There may be regions that apply to a J1 sample which don't exist on the hg38 reference sequence. If you have FastQ data from a WGS, then the previously unmapped reads are available and can be mapped to the new regions.
A re-mapping of the FASTQ reads from enriched Y chromosome sequencing (e.g. Y Elite or BigY) can be technically done, but we don't recommend it because it's unlikely that the selected reads will map to the new, unexplored regions of the CP086569.1 reference.

We're providing a mapping service for FastQ files from previously available YSEQ WGS data or 3rd party NGS data to CP086569 in a BAM file. Optionally we can extract the FastQ data from a BAM file in any other reference mapping format, but there is no warranty that all FastQ reads can be recovered if the unmapped reads are removed or low quality reads have been clipped.

Please provide us with the information how we can access / download your FastQ files in the comment field.

To transfer the large sequencing data files you have several options:

1.) You download the files on your computer, store them on a micro SD card and mail them to YSEQ.

2.) You download the files on your computer and upload them to a location where you can give us download access (e.g. Google Drive, Dropbox, Filemail etc.). Note that the files are big and free online accounts may not be big enough for all FastQ files that we need).

3.) We could configure a simple upload folder for you so that you can upload your files to our server. This is often problematic if you have a normal residential internet access because upload speeds are often slow and have frequent interruptions.

4.) You could give us access to your Third Party Company's account so that we download the files directly from them. We recommend to change the password before- and after this transaction.