User: msobol

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msobol10
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m*****@islander.tamucc.edu

Posts by msobol

<prev • 19 results • page 1 of 2 • next >
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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 26 days 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 27 days 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 4 weeks ago by msobol10 • updated 21 days ago by harish90
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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 11 weeks ago by msobol10 • updated 11 weeks ago by Vijay Lakhujani3.0k
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Comment: C: Combining Maker and Blast2Go
... I thought I should be concerned about the annotated GO's, which would be the blue bar. Out of the ~5,500 that were mapped, only 600 were annotated which to me seems low. ...
written 3 months ago by msobol10
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Comment: C: Combining Maker and Blast2Go
... Here is the pipeline I was using in case you were curious. [CGP Pipeline on Github][1] I was following the annotation pipeline made for not having RNA-seq data. The last step is using MAKER outputs to train Augustus, but I have been having issues with Augustus (link to my question on Biostars abou ...
written 3 months ago by msobol10
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Comment: C: Combining Maker and Blast2Go
... I am working with a deep sea sediment fungus "closely" related to *Penicillium chrysogenum*, so essentially it's a non-model organism (well from what I understand). It's possible that MAKER's results were low quality because I did not have RNA-seq data for this isolate. For MAKER, I used BUSCO to ...
written 3 months ago by msobol10
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Comment: C: Combining Maker and Blast2Go
... I am using Blast2GO Pro. I ran BlastP on my protein.fasta file from MAKER and then uploaded the .xml to Blast2GO. I mapped and annotated the .xml file, but my GO annotations were low (picture link below). Now I am wondering if it would be better to blast the transcript.fasta file from MAKER and then ...
written 3 months ago by msobol10
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Combining Maker and Blast2Go
... Hi, I was wondering what the correct way was to get gene function from MAKER's outputs? I was hoping to upload the files to Blast2GO to assign functionality from Blast and Interproscan. The using Blast2GO, I wanted to create some visuals such as piecharts with gene family abundances, etc. I tried ...
genome annotation fungi written 3 months ago by msobol10 • updated 3 months ago by lieven.sterck2.1k
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Comment: C: Softwares for gene annotation
... How to you input Maker's output into Blast2GO? I.e. what output file would you use and how would you annotate it in Blast2GO? Thanks! ...
written 3 months ago by msobol10

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