User: O.rka

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O.rka170
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Posts by O.rka

<prev • 207 results • page 1 of 21 • next >
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Why is hmmsearch only using the 1st HMM in a concatenated HMM database?
... I'm running `hmmsearch via HMMER 3.3` with a concatenated HMM file. Here is the first 1000 lines of my [tigrfams.hmm.gz](https://pastebin.com/raw/Qt0PrqvV). It looks like the file is properly merged with the following format: [HMM] // [HMM] // I don't know why but I'm only getti ...
protein domain hmmer hmm script bash written 21 hours ago by O.rka170 • updated 21 hours ago by Mensur Dlakic4.3k
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Comment: C: How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
... Ok interesting, it might be a good idea if I start using `-Z 45638612` to keep analysis pipelines fairly consistent. My last question...is the `score` affected by `-Z` or only the `E-value` calculation? ...
written 21 hours ago by O.rka170
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Comment: C: How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
... Thank you, this is extremely helpful. When you're saying database size do you mean the number of HMMs in an HMM database or the number of sequences used to create the database? Should I use the `-Z` flag used to build each PFAM individually for each hmmsearch run? For example, `PF10417.9` there ...
written 1 day ago by O.rka170
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Comment: C: How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
... I noticed a lot of wrappers use the `-Z` flag. How exactly would this influence the results? ...
written 1 day ago by O.rka170
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How to choose between --cut_ga, --cut_tc, and --cut_nc in hmmsearch? (hmmer)
... I'm trying to decide what would be the most appropriate threshold criteria? In particular, this is for PFAMs and a human metagenomics dataset. I'm curious what people have done in the past? It looks like anvio uses --cut_ga as the default. https://github.com/merenlab/anvio/issues/498 **What been ...
domain hmm alignment protein written 1 day ago by O.rka170 • updated 1 day ago by Mensur Dlakic4.3k
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Comment: C: How to get "best" taxon identifier from diamond output with staxids?
... That's a good point! I hadn't realized this is one of the shorter ORF calls. So in this case, would it have mapped equally well to 1227265 and 1227266? ...
written 2 days ago by O.rka170
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Comment: C: BLAST multiple staxids
... `staxids` doesn't work for `diamond` unfortunately. ...
written 2 days ago by O.rka170
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How to get "best" taxon identifier from diamond output with staxids?
... I recently discovered the `staxids` field with `diamond` (`staxid` is not a thing with `diamond`). I'm trying to assign taxonomy identifiers to all of my ORFs but I'm encountering many instances of when there are 2 or more (sometimes many more). **What is the recommended way for picking the "best" ...
metagenomics alignment protein diamond blast written 2 days ago by O.rka170
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How to compute module completion ratio of KEGG modules from KO identifiers? (command line)
... I was previously using [KEGG-MAPLE](https://www.genome.jp/tools/maple/) to compute module completion ratios for metagenome assembled genomes. However, this tool was web only (very frustrating) and also it has been discontinued. Now I'm trying to do something similar but I would like to automate ...
database written 3 days ago by O.rka170
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Comment: C: How can I get taxonomy identifiers (staxids) using diamond? (Error: Invalid outp
... Wow, it's running now. Sorry, I should have tried that before posting. All of the examples with blast I saw required the quotes. Thank you! ...
written 3 days ago by O.rka170

Latest awards to O.rka

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Epic Question 9 weeks ago, created a question with more than 10,000 views. For How to tell bloodtype from SNPs data?
Popular Question 3 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Voter 3 months ago, voted more than 100 times.
Scholar 4 months ago, created an answer that has been accepted. For A: Can you assemble with merged paired end reads and unmatched reads as "single end
Popular Question 4 months ago, created a question with more than 1,000 views. For Gene ontology-type analysis but with protein domain IDs? (e.g. TIGRFAM, PFAM)
Popular Question 6 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Popular Question 9 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Scholar 11 months ago, created an answer that has been accepted. For A: Can you assemble with merged paired end reads and unmatched reads as "single end
Popular Question 11 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Scholar 12 months ago, created an answer that has been accepted. For A: Can you assemble with merged paired end reads and unmatched reads as "single end
Centurion 12 months ago, created 100 posts.
Popular Question 14 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Popular Question 15 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 17 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Scholar 17 months ago, created an answer that has been accepted. For A: Can you assemble with merged paired end reads and unmatched reads as "single end
Popular Question 19 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 19 months ago, created a question with more than 1,000 views. For Most up-to-date Gene Ontology [GO] analysis?
Great Question 23 months ago, created a question with more than 5,000 views. For How to tell bloodtype from SNPs data?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?

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