Link to this post | posted 10 Jan, 2024 21:46
jcaoyao@gmail.com	Thank you very much.

Link to this post | posted 10 Jan, 2024 21:29
jcaoyao@gmail.com	Most thankful for your wonderful explanation, Dan! It does make sense. So having a Class 2 Biosafety Cabinet wouldn't make your lab a BSL2, and therefore, allow you to handle M. abscessus?

Link to this post | posted 10 Jan, 2024 09:45

jcaoyao@gmail.com

Happy New Year SEA PHAGES Community, Does anyone know where to find the ultimate, legal, and foolproof statement on whether Mycobacterium abscessus clinical strains can be handled in a BSL1 lab (and if there is any leeway* at all allowed)? All I know is pathogens that do not cause illness to healthy humans belong to BSL1 lab, and pathogens like tuberculosis that can cause illness to healthy humans belong to a BSL2 lab, but I would need a specific confirmation for M. abscessus. *For example, I have a BSL1 lab where there is biosafety cabinet of Class 2 that is functional though its air velocity may not be as high as it used to be because it is quite old. There are also Bunsen burners in the lab for working with M. abscessus on the bench. Much obliged! Edited 10 Jan, 2024 18:13

Link to this post | posted 27 Sep, 2023 12:04

jcaoyao@gmail.com

Thank you for this clear walk-through, which I understand is for assembling a genome from scratch. But supposing I have assembled already using 50k reads, and it has given me 100+ contigs of a variety of sizes, and I want to add the remainder of the reads that were not used initially, so as to improve the assembly and get the fewest contigs possible, you wouldn't know how I could do that, would you? Dan once said to use the command he posted at https://seaphages.org/forums/topic/42/ but all my attempts to execute it have failed. I do hope somebody eventually sees my query there. But since it is unlikely, would it be possible at all for me to send you my fastq files and run them on your computer, and possibly join the 100+ pieces of contigs? According to BLASTn, the contigs seem to belong to several different phages even within a single fastq file. I would be more than grateful.

Link to this post | posted 23 Sep, 2023 19:12

jcaoyao@gmail.com

Hi Dan and Lee, I'm having the same question. I tried executing the new command you posted modified to my case: addSolexaReads.perl -ace 454Contigs.ace.1.ace -fastqfof Reads.fof -fasta 454Contigs.ace.1.contigs.fof Since my files are called 454Contigs.ace.1.ace and 454Contigs.ace.1.contigs and Reads.fof. But it still wouldn't work, including different variations I tried. Are there any key preceding steps that I should know that are not in your tutorials? I couldn't find that video with the comments at the bottom that you mentioned. Thanks very much.

Link to this post | posted 21 Sep, 2023 09:21
jcaoyao@gmail.com	Hi, cdshaffer. I have tried to add Illumina reads to an assembly using "addSolexaReads.perl" and following Dan's instructions. However I keep getting the following error "-ace must be specified". Everything looks correct to me with the command and filenames. Any idea?

Link to this post | posted 19 Sep, 2023 16:32
jcaoyao@gmail.com	Got it, thanks for your wishes. Now with 5 GB, it has been going on for over 6 hours and it is getting stuck at the last few hundred reads. I had downsampled to 200,000 lines. I think I'm gonna abort and I try 100,000 to get 50x coverage, since it is the bare minimum, which shouldn't take me more than an hour. Edited 19 Sep, 2023 19:58

Link to this post | posted 18 Sep, 2023 20:45
jcaoyao@gmail.com	Thank you for your clear and most helpful indications. Now I can move my slider. The green area of the ruler below my slider only goes up to about 5 GB. I guess I'll have to live with that.

Link to this post | posted 18 Sep, 2023 19:15
jcaoyao@gmail.com	Thank you, Professor. I am running Newbler using the 2017 SEA VM in virtualbox on my hp laptop Windows 11 Home. I went to the same place you said, Machine -> settings -> System -> motherboard, but all the writings are in colorless (grey), so the slider or anything else cannot be adjusted in any way. Would there be a different way?

Link to this post | posted 18 Sep, 2023 09:53
jcaoyao@gmail.com	You're right, I would like to know how to increase the memory available. Are you talking about RAM memory? What specifications should the ideal computer have for this sort of job? Edited 18 Sep, 2023 09:55