User: luyang1005

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luyang100520
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Posts by luyang1005

<prev • 36 results • page 1 of 4 • next >
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kegg orthology entry to pathway ko
... Hi, community, I have used EggNOG produce a table(as shown below) which contains the kegg orthlogy entry. May I know how to get the pathway name(or pathway modules) based on the list column? Like ABC transporters,methane metabolism,ect Thanks in advance. query list k119_1151408_63 K00864 k119_115 ...
genome gene written 3 months ago by luyang100520
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conserved protein finding
... Hi, community, I am analyzing the shotgun metagenomics data. I have got the scaffolds from the assembly. And I have got the protein hits to Pfam database. Since some papers mentioned that use conserved protein to predict taxonomy, which could be more reliable. May I know how to get the conserved pr ...
genome assembly written 3 months ago by luyang100520
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Comment: C: shotgun metagenomics assembly
... I see. Thanks for your answers. ...
written 4 months ago by luyang100520
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taxonomic assignment of metagenomic bins and detect 16S rRNA gene in metagenomic bins
... Hi, community, I have Hiseq metagenomic data. I have used MEGAHIT assembly the reads, then I binned the contigs which results to 500 bins. I have used CheckM to assess the genome bins. All bins with <10% contamination and >70% completeness were saved and BLASTN to SILVA 132 SSU database. Most ...
assembly next-gen written 4 months ago by luyang100520
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Comment: C: shotgun metagenomics assembly
... Thanks so much for the suggestions. I will go ahead on protein prediction and annotation to have a look. Yesterday I have done one sample's binning. And I checked it with CheckM, it seems that only binning for each sample I can get 30 (total76) bins with completeness> 90% and contanmination< ...
written 4 months ago by luyang100520
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Comment: C: shotgun metagenomics assembly
... Hi, Carambakarocho, Thanks for your reply. My purpose is to know what taxonomy is there and do get some functional characterization of the samples. My samples are anaerobic manure samples. I have got the 25000 contigs from IDBA and MEGAHIT, 44000 contigs from metaSpades. Each software has weak indic ...
written 4 months ago by luyang100520
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Comment: C: shotgun metagenomics assembly
... Yes, the first paper is helpful. Thanks. But I still do not know whether my assembly is Ok or not. Since my raw fastq reads after trimmomatic is 35G, while after assembly, it is 200M. Anything wrong? ...
written 4 months ago by luyang100520
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shotgun metagenomics assembly
... Hi, community, I am dealing with shotgun metageomincs data with 100bp paired-end reads from Hiseq. I have used the default setting in metaSPAdes, IDBA and MEGAHIT to assemble the reads. But I do not know which one is better. Any suggestions? Are there any indicators to evaluate it? Even I know som ...
assembly next-gen written 4 months ago by luyang100520 • updated 4 months ago by dllopezr20
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shotgun metagenomics result evaluation
... Hi, I am new to shotgun metagenomics analysis. However, I have used Metaphlan2, kraken, minikraken to try on my samples. The results are totally different. Especially, Metaphlan2 is different from the other two. Even kraken and minikraken differ some. Therefore, now I do not know which result is ...
next-gen sequencing written 4 months ago by luyang100520 • updated 12 weeks ago by Biostar ♦♦ 20
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much different result from shotgun metagenomics and 16S amplicon
... Hi, community, I am analyzing the taxonomic profiling of my shotgun data. Which are 100bp paired-end reads from Illumina Hiseq. Now I am using Metaphlan2 to do the metagenomics profiling. However, the profiling result is far away from Illumina 16S miseq results. Since I have also been using Illumin ...
sequencing written 5 months ago by luyang100520

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