User: ARich

gravatar for ARich
ARich80
Reputation:
80
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Location:
United States
Last seen:
3 months, 1 week ago
Joined:
6 years, 4 months ago
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Posts by ARich

<prev • 43 results • page 1 of 5 • next >
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Comment: C: Diamond blastp output
... Yes i did try R package called "rentrez" ``` search <- entrez_search(db="protein", term="WP_129184883[Accn]") (links <- entrez_link(dbfrom="protein", db="nuccore", id=search$ids) links$links$protein_nuccore_wp ``` This provides me taxid. But I am looking for something where the diamond blast ...
written 3 months ago by ARich80
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Diamond blastp output
... Dear Biostar user, I have a question regarding diamond output. I ran diamond blastp on my contigs against NR database. After this i used diamond view to convert m8 format. In this m8 file, the subject seqid is something like "WP_129184883.1" although i was expecting the genbank ID gi|...|. Can so ...
assembly sequence written 3 months ago by ARich80
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Comment: C: Functional annotation of metagenomic contigs
... Thank you for detailed explanation. Its was really helpful. As you mentioned to publish one need more rigorous analysis. Can you suggest any good paper showing this section in detail? ...
written 3 months ago by ARich80
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Comment: C: Functional annotation of metagenomic contigs
... This is really of great help. I am taking oppurtunity to ask more :) Actually CheckM provides very low resolution classification and I order to have better resolution I was running blastn with Nt database on each combined bin (as shown below). Do you think its a good idea to do so? Or can you recomm ...
written 3 months ago by ARich80
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Comment: C: Functional annotation of metagenomic contigs
... That you for this detailed reply! You recommend prokka as well! Question: Should your recommend to contatenate all checkM bins to create one single file which can then be used as a input for prokka? or Do you run prokka on individual bins? What is recommended to classify bins for taxonomy? Cheers ...
written 3 months ago by ARich80
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Comment: C: Functional annotation of metagenomic contigs
... Thank you for the reply. Question: 1. Can prokka take all kingdom like this --kingdom 'Archaea|Bacteria|Mitochondria|Viruses' ? 2. Can I also use prokka on bins from Maxbin2 output? If yes then, should it be called on each bin similar to how it is called on contigs? ...
written 3 months ago by ARich80
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Functional annotation of metagenomic contigs
... Dear Biostar users, Its a very naive question but i certainly lack some clarity here. I have contigs from megahit and would like to perform functional annotation. For this purpose i first used prodigal for gene prediction and the prokka for annotation. My question here is if I would like to do fun ...
assembly written 3 months ago by ARich80
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Answer: A: Samtools sort error
... The issue is resolved. I had installed the samtools through conda and it did not install HTSLIB and that was the issue. Now I have installed samtools locally and it ran normally. Thank you helping me think beyond the script. Cheers, AR ...
written 3 months ago by ARich80
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Comment: C: Samtools sort error
... Yes its there. Isn't that correct? ...
written 3 months ago by ARich80
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Comment: C: Samtools sort error
... Thank Pierre for the reply, Yes it is sam.gz. Nonetheless, I also tried without compression verison and I still got the error message during sorting ...
written 3 months ago by ARich80

Latest awards to ARich

Scholar 3 months ago, created an answer that has been accepted. For C: CluserProfiler message "No gene can be mapped"
Popular Question 19 months ago, created a question with more than 1,000 views. For kmer for sample list
Popular Question 19 months ago, created a question with more than 1,000 views. For How to estimate the metagenome size
Popular Question 19 months ago, created a question with more than 1,000 views. For Unequal Sample Number
Scholar 19 months ago, created an answer that has been accepted. For C: CluserProfiler message "No gene can be mapped"
Popular Question 3.4 years ago, created a question with more than 1,000 views. For How to estimate the metagenome size

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