User: flavobacteria

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Posts by flavobacteria

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Answer: A: Can we assembly the draft sequences that is assembled by another genome assemble
... 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 flavobacteria50
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Comment: C: Can we assembly the draft sequences that is assembled by another genome assemble
... 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 flavobacteria50
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Can we assembly the draft sequences that is assembled by another genome assembler
... 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 ...
genome assembly next-gen sequencing written 3.5 years ago by flavobacteria50
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Genome sequence assembly for fungi by Abyss
... 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? ...
assembly written 3.6 years ago by flavobacteria50
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Comment: A: For ABySS, I have a question for file that the assembly will go to
... 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 flavobacteria50
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For ABySS, I have a question for file that the assembly will go to
... 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 ...
genome assembly next-gen sequence sequencing written 3.6 years ago by flavobacteria50
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Comment: C: please help look at the output for my assembly of bacterial genome using DNASTAR
... what do you want to comment on it? Thank you ...
written 4.2 years ago by flavobacteria50
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please help look at the output for my assembly of bacterial genome using DNASTAR
... 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 ...
assembly forum written 4.2 years ago by flavobacteria50 • updated 4.2 years ago by Michael Dondrup47k
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remove the singletons using remove.rare in mothur
... 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 ...
next-gen sequencing written 4.3 years ago by flavobacteria50
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How to create functional categories of genes after obtaining annotation
... 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 ...
forum rna-seq written 4.5 years ago by flavobacteria50 • updated 4.5 years ago by genomax90k

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