-
|
Hi, i loaded a fasta file via the cli and after some time it said it was succesful. but now when i wanto to add a linear genome view in the web interface it shows me a circling loading thingy, but nothing happens. is this supposed to load that long? |
Beta Was this translation helpful? Give feedback.
Replies: 1 comment 15 replies
-
|
can you check what version you are using? the 1.3.1 release of jbrowse 2 included a fix (#2060) that improved performance for assemblies that have many contigs for example, loading even a Pine tree genome with hundreds of thousands of scaffolds is pretty quick ~3 seconds after downloading the 60mb file |
Beta Was this translation helpful? Give feedback.
-
|
https://www.g3journal.org/content/9/7/2039 thats the genome i want to visualize, and they state that its very fragmented, so thats probably it |
Beta Was this translation helpful? Give feedback.
-
|
interesting... it looks at least about 10x more fragmented than the p.taeda which was our previous benchmark for loading large fragmented assemblies. N50 of 14kb vs >200kb ...there might be some way we could help as it may not really be strictly necessary to load the fai file on startup. let us know if you think that might be useful |
Beta Was this translation helpful? Give feedback.
-
|
that sounds good, but maybe the fragmented nature of the genome is the main problem? i guess the fai has to be loaded at some point, so the problemn that it is too big might not be solved? and unrelated because im a real beginner in this field, what would you recommend to "simplify" the fai file? to i have to reassembly it or can i edit the fasta somehow? |
Beta Was this translation helpful? Give feedback.
-
|
It is hard to say. You could potentially filter small contigs like this https://www.biostars.org/p/129796/ another option would be to arbitrarily join some of the contigs, separated by gaps of Ns, into fake scaffolds. this would not be lossy operation like filtering it out, but would potentially be a little confusing the ideal thing would be for a group to make a new genome assembly incorporating long reads or hi-c to assist with joining the fragments together |
Beta Was this translation helpful? Give feedback.
-
|
Okay that biostars link did the trick, the fai is now ~50mb and loads just fine. Thanks for your help! |
Beta Was this translation helpful? Give feedback.
can you check what version you are using? the 1.3.1 release of jbrowse 2 included a fix (#2060) that improved performance for assemblies that have many contigs
for example, loading even a Pine tree genome with hundreds of thousands of scaffolds is pretty quick ~3 seconds after downloading the 60mb file