Link to this post | posted yesterday, 19:33

nietof

Hi everyone I am new to ONT. While I understand the sequence may not be up to par with Illumina for annotation purposes, I still want to use for class purposes. I used the rapid sequencing kit with PCR barcodes https://nanoporetech.com/document/rapid-sequencing-dna-v14-pcr-barcoding-sqk-rpb114-24 with a flongle flow cell. I sequence 21 phages including a lambda as control. have the reads for all the phages now and I need help on how to proceed with assembly. The ONT website is not very good to find specific answers. Is anybody able to share a protocol from reads to assembly and cluster assignment? Thank you Fernando

Link to this post | posted 02 Jan, 2025 16:44
nietof	HI Dan Happy New Year I use a Mac and I needed to use DNA Master. I usually use a PC laptop but I didn't have it with me. Thank you Regards to everyone at UPitt ans SEA-PHAGES Fernando

Link to this post | posted 22 Dec, 2024 15:14
nietof	Happy Holidays The instructions on the website say that the unzipped SEA VM should be 11GB but on my mac the size is only 2.45GB. When I install it following the instructions I get this error: "error attempt to read or write outside disk hd0" thank you Fernando

Link to this post | posted 30 Sep, 2024 18:12

nietof

viknesh nietof Hi everyone Has anybody successfully isolated phages from soils stored frozen after sampling? Thank you Fernando Wanted to share that no faculty has shared with me that they've tried this. Hi Vic thanks for the reply,I found a citation from an seaphages abstract, I think from a student or faculty at UPitt, that isolated phages from frozen soils during the winter of 2023. But she isolated them actually from outdoor frozen soils. I was going to try to isolate from soils in storage at -80C. thank you F

Link to this post | posted 30 Sep, 2024 14:51
nietof	Hi everyone Has anybody successfully isolated phages from soils stored frozen after sampling? Thank you Fernando

Link to this post | posted 11 Apr, 2024 17:42
nietof	Hi everyone We have a putative holin in Alkhayr cluster O gene 66 in PECAAN. Both TmHmm and Sosui show two tmb domains, strong matches in BLAST to other phages in this cluster and others but HHPred doesnt yield robust matches to a holin protein. It has Lysin a and b upstream. I assume it is a Holin but I am not sure why HHPred doesnt find matches.

Link to this post | posted 11 Apr, 2024 17:42
nietof	Hi everyone We have a putative holin in Alkhayr cluster O gene 66 in PECAAN. Both TmHmm and Sosui show two tmb domains, strong matches in BLAST to other phages in this cluster and others but HHPred doesnt yield robust matches to a holin protein. It has Lysin a and b upstream. I assume it is a Holin but I am not sure why HHPred doesnt find matches.

Link to this post | posted 03 Apr, 2024 15:07
nietof	lhughes It opened fine for me just now. Lee I just checked and it works for me now too. Thank you F

Link to this post | posted 03 Apr, 2024 13:27
nietof	Hi everyone Anybody having problems accessing phamerator. I haven't been able to access it since yesterday. It doesn't go beyond the sign in page. Thank you Fernando

Link to this post | posted 03 Apr, 2024 13:23
nietof	Hi We are annotating a cluster O phage, Alkhayr. Our sequence is not canonical. Furthermore, HHPred doesn't support calling TAC as a function for either one of the gene products (gene 50 and 51). I have attached the HHPred matches for gene T, gene 50. Regards F 210Kb