User: msobol

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msobol0
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Posts by msobol

<prev • 15 results • page 1 of 2 • next >
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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 8 days ago by msobol0
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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 9 days ago by msobol0
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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 9 days ago by msobol0
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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 10 days ago by msobol0
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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 11 days ago by msobol0 • updated 10 days ago by lieven.sterck1.4k
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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 11 days ago by msobol0
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Comment: C: Augustus Segmentation fault error message
... Yes. This is now the HPC cluster is set up at my university. The autoAug.pl script works fine up until the part where it tries etraining. So I do not think there is anything wrong with how I am calling the autoAug script. ...
written 12 days ago by msobol0
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Augustus Segmentation fault error message
... I am waiting to hear back from the developer of Augustus, but I wanted to see if anyone else had experience with the error message I received. First try with etraining: etraining --species=1371E14H2 training.gb.train >train.out ...sh: line 1: 118112 Segmentation fault etraining --speci ...
augustus annotation gene prediction written 14 days ago by msobol0 • updated 14 days ago by Ram15k
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Comment: C: MAKER annotation pipeline output
... I did, but it does not seem that the option exists. Oh well, thanks anyways. ...
written 16 days ago by msobol0
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Determining ploidy from fungal genomes
... Hi, I am working on fungal isolates from deep-sea sediments. It is debated on whether these isolates are haploid or diploid. I was wondering if there was a way to determine if they were either haploid or diploid using some type of bioinformatics tool. I did try assembling the genome using both S ...
genome assembly diploid haploid fungi written 16 days ago by msobol0 • updated 13 days ago by Carambakaracho210

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