User: msobol

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msobol10
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Posts by msobol

<prev • 37 results • page 1 of 4 • next >
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Comment: C: Top hit from phmmer
... I don't think I understand your question. I used a protein fasta file made up of all the predicted genes in my genome. When I searched it against the MEROPS database, it gave me over 100 matches for each gene. I only want phmmer to give me the top hit from the MEROPS database, based on the evalue, ...
written 2 days ago by msobol10
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Comment: C: Genome Guided Transcriptome assembly
... So I think I was able to clear up what I was confused about with the mapping versus assembly approach. So since we have a reference genome, there is no need to do an assembly. My only remaining question is if you are supposed to map the RNA sequence reads to the repeat-masked genome assembly or the ...
written 3 days ago by msobol10
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Comment: C: Genome Guided Transcriptome assembly
... Okay, let me see if I understand what you are saying. So you suggest instead of using the reference genome to assemble the RNAseq reads, I would just map the raw reads to the reference genome. If that is the case, then what is the difference I guess in mapping the reads vs. assembling them? Is there ...
written 3 days ago by msobol10
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Genome Guided Transcriptome assembly
... Hi, I recently de-novo assembled a non-model fungal genome using PacBio and Illumina reads, but now we have new RNA-seq data that needs to be assembled. I figured the best way to assemble the transcriptome would be to use a genome guided assembler like Trinity...unless you guys recommend a differe ...
genome assembly rna-seq transcriptome written 4 days ago by msobol10 • updated 4 days ago by Buffo1.3k
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Comment: C: data assembling and analysis for polyploid plant
... *I hope this appropriate for me to comment... I am working with a non-model fungus and also have this question. This is the first time I have dealt with whole genome assembly and annotation of diploid organisms. I compared assemblies from SPAdes and dipSPAdes (diploid version of the assembler) and ...
written 6 days ago by msobol10
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Top hit from phmmer
... Hey guys, I have googled this and can not find any advice or answer. Hopefully, I have not overlooked it. I need phmmer to only write the top hit for each query I provide. Currently, it provides over a 100 hits for almost every query, which I have 12,000 of. It would take me way too much time to so ...
gene annotation phmmer hmmer genome written 8 days ago by msobol10
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Comment: C: KOG/COG annotation results chart
... I found this script super helpful, thank you! I do have a few questions though. 1. Is there a way to get rid of the awkward space between the first y major axis tick (0) and the x axis? 2. Do you know how you would add a second legend, like the bottom legend in this [pic?][1] Thanks! [1]: http ...
written 16 days ago by msobol10
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Comment: C: Mapping Gene Positions onto a Genome
... Sorry, I thought I replied, but it is eukaryotic, fungal to be exact. The query file is a multi-fasta file. Like this: >1371E_00011828-RA protein AED:0.07 eAED:0.07 QI:0|0|0|0.75|1|1|4|0|184 MLIYTDIVSGDEIVADTFNLVPNKDFDILWECDCRKYLKRSNEDFQLEGANPSAEDAEDD GGEGEATMVHDIEDQFRLVWLKVEDGAKPS ...
written 16 days ago by msobol10 • updated 16 days ago by genomax63k
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Comment: C: Mapping Gene Positions onto a Genome
... Here is what the output looks like [eggNOG][1] [1]: https://photos.app.goo.gl/V4VGxZqESKiJ6Pak9 ...
written 16 days ago by msobol10
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Comment: C: Mapping Gene Positions onto a Genome
... I did, but it was different fro that paper which was based on metatranscriptomics. Mine are based on whole genomes. I used MAKER for gene predictions. I uploaded the protein fasta file from the MAKER output into the [eggNOG mapper][1] [1]: http://eggnogdb.embl.de/#/app/home ...
written 16 days ago by msobol10

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