User: FAST_GENOME

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FAST_GENOME50
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Posts by FAST_GENOME

<prev • 21 results • page 1 of 3 • next >
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Comment: C: How to comparing two bacterial genomes and find the mutation, rearrangement etc.
... Appreciate your help. ...
written 3 months ago by FAST_GENOME50
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Comment: C: How to comparing two bacterial genomes and find the mutation, rearrangement etc.
... Thank you so much. I just find an available genome on NCBI. Can I map the reads from two strains against the genome ref and filter the mutation only exist in the biocide resistance strain? Thanks. ...
written 3 months ago by FAST_GENOME50
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How to comparing two bacterial genomes and find the mutation, rearrangement etc.
... Dear All, we have two different strains of bacteria. One has biocide resistance and another one doesn't. We try to find out which and how many mutations are involved in the resistance. I am thinking of sequencing the 2 strains and compare each other. I am not sure if this is a correct idea. Can some ...
gene written 3 months ago by FAST_GENOME50 • updated 3 months ago by jrj.healey7.6k
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Comment: C: What is the normal N50 range when assembly the virus genome.
... Thank you so much. I will do that. I just check the ddbuk manual, should I use the following command line? Can you please give me some pointer. The virus genome is about 9k. $ bbduk.sh in=reads.fq out=unmatched.fq outm=matched.fq literal=ACGTACGTACGTACGTAC k=18 mm=f hdist=2 ...
written 3 months ago by FAST_GENOME50
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Comment: C: What is the normal N50 range when assembly the virus genome.
... Thank you so much for your replying and information. ...
written 3 months ago by FAST_GENOME50
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Comment: C: What is the normal N50 range when assembly the virus genome.
... wow, how did you know the assembly contigs all from human mitochondrial? The total contigs are 478. The largest one is 14128. but the genome of the virus is about 9k. I blasted about 2k raw reads and random pick 80-100 assembled contigs, they all belong to Human. ...
written 3 months ago by FAST_GENOME50
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Comment: A: What is the normal N50 range when assembly the virus genome.
... Dear all, I blast my assembly contig and all are Homo sapiens mitochondrion. Is that a host genome contamination? Thanks ...
written 4 months ago by FAST_GENOME50
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Comment: C: What is the normal N50 range when assembly the virus genome.
... Thanks. Let me blast the assembly first. And a quick question about "map reads to viral contigs and re-assemble". Which tools do you recommend? and how to evaluate the results? ...
written 4 months ago by FAST_GENOME50
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Comment: C: What is the normal N50 range when assembly the virus genome.
... Thanks, I will try and update the results. ...
written 4 months ago by FAST_GENOME50
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Comment: C: What is the normal N50 range when assembly the virus genome.
... Thanks. I am trying the following command and will update the results when it finishes. The genome is about 9k. $spades -o spades_out --12 trimmed.fq --careful & $spades -o spades_out --12 normalized.fq --careful ...
written 4 months ago by FAST_GENOME50

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