Analyses in organisms possessing ATGC at the end of chromosomes

[toshwatatosh]

We are now working on Nanoseq in a monkey. Human and mouse chromosomes usually start with N. But, in this monkey, some chromosomes start with ATGC. When sequence reads are mapped to the end of such chromosomes, errors happen at the dsa step. To avoid this problem, we remove reads at the ends of the chromosome. Could this removal affect the final mutation burden rate or other results?

[fa8sanger]

Thank you! We are aware of that problem, and there’s a branch (hotfix/3.5.8) fixing it. And if you are brave to try untested versions, we also have this forked repo with some recent fixes (https://github.com/fa8sanger/NanoSeq/tree/develop) Regarding your creative solution, that should work perfectly, no problem at all. On 22 Nov 2024, at 09:08, toshwatatosh ***@***.***> wrote: We are now working on Nanoseq in a monkey. Human and mouse chromosomes usually start with N. But, in this monkey, some chromosomes start with ATGC. When sequence reads are mapped to the end of such chromosomes, errors happen at the dsa step. To avoid this problem, we remove reads at the ends of the chromosome. Could this removal affect the final mutation burden rate or other results? — Reply to this email directly, view it on GitHub [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_cancerit_NanoSeq_issues_107&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=v9-R7fUmjpv-9Zaqyk1nlnlOC3qPkTEJz5tyYxg2uec&m=BoQpb05shzifW4VJerj1tgEgl0mXdJCmyfMKk39aWz40PJSV3klVaObwl1ZY42Im&s=UQkzU_2vcP4l3ftdVneteWHW1Bwu1CLpQSlB546r32o&e=>, or unsubscribe [github.com]<https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ADNUT3LG5H47ZTECE6I3YGT2B3X7TAVCNFSM6AAAAABSI4FVO2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGY4DENBZHE3DOOI&d=DwMCaQ&c=D7ByGjS34AllFgecYw0iC6Zq7qlm8uclZFI0SqQnqBo&r=v9-R7fUmjpv-9Zaqyk1nlnlOC3qPkTEJz5tyYxg2uec&m=BoQpb05shzifW4VJerj1tgEgl0mXdJCmyfMKk39aWz40PJSV3klVaObwl1ZY42Im&s=K2T3zMVouxa1akknOm4hnNs0h-_lbSGd7a2nzHacXO0&e=>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

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