All Questions
5
questions
2
votes
1
answer
45
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How good does the assembly of an NCBI prokaryotic genome have to be in order to argue gene loss?
NCBI has several labels for assembly completeness - Complete, Scaffold, Chromosome and Contig. Complete would be a circularized genome (or linear, rarely)
For a Complete genome it's fairly ...
- 1,007
1
vote
1
answer
565
views
where to find sample contig data
Where or How can I find contigs? I am trying to learn Bioinformatics and I want to make a reference-based gene search. I also want to align contigs with a given reference sequence. From NCBI other ...
- 73
1
vote
1
answer
197
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Comparing gene abundances between metagenomes
My workflow until now:
Find fragments of a marker gene in unassembled metagenomes > download and assemble metagenomes > recover the gene neighborhood / gene set of interest
Right now I have a ...
- 1,007
2
votes
1
answer
46
views
Assemble reads for a specific gene
I have a lot of unassembled sequencing data and I want to build phylogeny for some genes from these data. I can retrieved the sequene by mapping reads to a reference sequence but if the two species ...
- 127
1
vote
1
answer
296
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Will using smaller kmers help get larger contigs? If not, then what?
I've been using MEGAHIT to assemble metagenomes, with particular focus on specific genomic areas.
Sometimes all I get is gene fragments or pathway fragments (eg. if I know that genes A, B, C, D and E ...
- 1,007