User: msobol

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msobol10
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Posts by msobol

<prev • 26 results • page 1 of 3 • next >
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Normalizing CAZy data
... Hi, I am annotating two fungal genomes. I have run the genomes through dbCAN database to determine how many of the putative proteins encode CAZy enzymes, but now I am trying to figure out if I can simply report the relative abundance of the genes for each genome, or if I need to show some sort of ...
genome annotation cazy fungi enzymes written 5 weeks ago by msobol10
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Comment: C: Targeted Loci BLAST: No Significant Similarity Found
... I gotcha. Thanks for clarifying. ...
written 3 months ago by msobol10
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Comment: C: Targeted Loci BLAST: No Significant Similarity Found
... *she I have not yet tried making database based on my genome. I had previously uploaded my genome to the NCBI BLAST website and blasted it that way. I am still surprised that I would not get a hit. My largest contigs are > 500,000 bp. I will also look into RNAmmer, thanks for the suggestion! ...
written 3 months ago by msobol10
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Comment: C: Targeted Loci BLAST: No Significant Similarity Found
... BUSCO can predict how complete a genome is based on the number of conserved orthologs. ...
written 3 months ago by msobol10
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Targeted Loci BLAST: No Significant Similarity Found
... I have two fungal genomes that I blasted against the ITS, 18S, and 28S targeted loci database in NCBI. You would think that somewhere in the genome would have a hit against either of these databases, but for some reason, I am not finding any hits. If there is a hit, the query coverage is below 10%. ...
ncbi genome fungi blast written 4 months ago by msobol10
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Comment: C: Opinion on best way to taxonomically classify a genome
... Based on the 18S rRNA we know it's closely related to *Penicillium*, however, these genomes are from environmental samples so there is uncertainty about how closely related the entire genome is to the reference. From what I can understand, you compare the genome to several reference genomes you bel ...
written 4 months ago by msobol10
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Opinion on best way to taxonomically classify a genome
... Hello, I am trying to taxonomically classify two fungal genomes. I have read a couple ways to do this. 1. Align the genome to reference genomes using programs such as Mummer or Muscle, then build a maximum likelihood tree with RaxML. 2. Determine common orthologs with Busco or Cegma from the g ...
genome orthologs taxonomy phylogenomics written 4 months ago by msobol10 • updated 4 months ago by Carambakaracho670
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Comment: C: Confused on PacBio outputs
... It says that the fastq files are the pre-filtered subreads and that's okay to use? ...
written 5 months ago by msobol10
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Confused on PacBio outputs
... Hi, I am trying to figure out which PacBio output to use for SPAdes hybrid assembly. I was given the three .bax.h5 files, the one .bas.h5 file, and the three fastq/fastq files. I have read that currently, the reads are stored in the three .bax.h5 files. So I was going to concat these files and c ...
long read assembly pacbio genomics written 5 months ago by msobol10
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To reassemble Illumina and PacBio, or just upgrade previous assembly with PacBio?
... Hi, I previously assembled a fungal genome with Illumina Hi-Seq paired-end sequences. The assembly was ~ 32Mbp and was made up of ~ 400 contigs. I did not try to join the contigs into scaffolds. BUSCO determined that the assembly was ~98% complete based on the number of orthologs. However, I jus ...
genome assembly pacbio illumina written 6 months ago by msobol10 • updated 5 months ago by harish140

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