User: flavobacteria
flavobacteria • 50
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Posts by flavobacteria
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... Can anyone help with this command
spades.py --trusted-contigs mtla90-contigs.fa o all
It gives error messages:
== Error == you should specify at least one unpaired, paired-end, or high-quality mate-pairs library!
I used the --trusted-contigs, why it still asks for one unpaired, paired-end, or hig ...
written 3.5 years ago by
flavobacteria • 50
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... It is fungal genome. When I run SPAdes, it aborts in the middle. I assume SPAdes is not perfect for this. ...
written 3.5 years ago by
flavobacteria • 50
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... If I have already assembled the genome sequences with a lot of contigs and short readings, can I use another software to further assembly the one that was assembled?
I used abyss to do the 1st round, but I have a lot of short readings.
If I use SPAdes to continue to assembly ... will it do any bet ...
written 3.5 years ago by
flavobacteria • 50
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... For k mer, what should I use? how do I decide to use k=25, 30 or more? Whether I need to try a different k values? ...
written 3.6 years ago by
flavobacteria • 50
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... Thank you for replying. My data set is really large (fungi genome). what I am asking is where really "ecoli " here comes from? We give? if we give the name, how the software knows where it locates (or simply the Abyss think it should be the same folder in the "in" file. Thank you again. ...
written 3.6 years ago by
flavobacteria • 50
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... Assembling a paired-end library
To assemble paired reads in two files named reads1.fa and reads2.fa into contigs in a file named ecoli-contigs.fa, run the command:
abyss-pe name=ecoli k=64 in='reads1.fa reads2.fa'
The parameter in specifies the input files to read, which may be in FASTA, FASTQ, qs ...
written 3.6 years ago by
flavobacteria • 50
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... what do you want to comment on it? Thank you ...
written 4.2 years ago by
flavobacteria • 50
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... SeqMan NGen Assembly Report
SeqMan NGen 13.0.0 build 359
Assembly Time: 1:41:54
Assembly Totals
Contigs: 308
Contigs > 2K: 151
Contigs To Reach Genome Length 6000000: 309
Contigs removed due to small size: 99692
Assembled Sequences: 1329497
...
written 4.2 years ago by
flavobacteria • 50
• updated
4.2 years ago by
Michael Dondrup ♦ 47k
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... Can you please advise if the following steps will do the job? Many thanks. If not, could you please also give us some suggestions (especially which commands should be used, and at which steps).
Thanks.
I did these:
Following mothur SOP,
1. mothur > sub.sample(shared=stability.an.shared, siz ...
written 4.3 years ago by
flavobacteria • 50
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... I got the annotation done and had the full list of gene expression. So, next, I want to create a Figure like this paper (Fig. 2). What should I do? Thank you.
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068298 ...
written 4.5 years ago by
flavobacteria • 50
• updated
4.5 years ago by
genomax ♦ 90k
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