User: msobol

gravatar for msobol
msobol10
Reputation:
10
Status:
New User
Location:
Last seen:
18 hours ago
Joined:
7 months, 1 week ago
Email:
m*****@islander.tamucc.edu

Posts by msobol

<prev • 25 results • page 1 of 3 • next >
0
votes
0
answers
141
views
0
answers
Comment: C: Targeted Loci BLAST: No Significant Similarity Found
... I gotcha. Thanks for clarifying. ...
written 19 days ago by msobol10
0
votes
0
answers
141
views
0
answers
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 20 days ago by msobol10
0
votes
0
answers
141
views
0
answers
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 20 days ago by msobol10
1
vote
0
answers
141
views
0
answers
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 25 days ago by msobol10
0
votes
1
answer
185
views
1
answers
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 6 weeks ago by msobol10
1
vote
1
answer
185
views
1
answer
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 6 weeks ago by msobol10 • updated 6 weeks ago by Carambakaracho550
0
votes
0
answers
174
views
0
answers
Comment: C: Confused on PacBio outputs
... It says that the fastq files are the pre-filtered subreads and that's okay to use? ...
written 11 weeks ago by msobol10
1
vote
0
answers
174
views
0
answers
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 11 weeks ago by msobol10
6
votes
3
answers
492
views
7 follow
3
answers
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 3 months ago by msobol10 • updated 11 weeks ago by harish130
0
votes
1
answer
239
views
1
answer
Taxonomy assignment from draft genome
... Hi, I have two assembled and annotated draft genomes of non-model fungal species. Based on the previous 18S analysis, they were both found to be closely related to Penicillium. Now that I have the genome, I wanted to assign taxonomy. What is your preferred way of assigning taxonomy from draft ge ...
genome taxonomy whole genome fungi written 4 months ago by msobol10 • updated 4 months ago by Vijay Lakhujani3.1k

Latest awards to msobol

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1739 users visited in the last hour