User: O.rka

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O.rka120
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Posts by O.rka

<prev • 165 results • page 1 of 17 • next >
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How to use anvio's gzipped HMM externally with HMMER?
... I'm trying to use this HMM that I have with my installation of Anvio using just HMMER: https://github.com/merenlab/anvio/blob/master/anvio/data/hmm/Bacteria_71/genes.hmm.gz I've went through the source code below but it's not very clear how it's running: https://github.com/merenlab/anvio/blob/mast ...
binning hmm anvio written 20 days ago by O.rka120 • updated 20 days ago by h.mon28k
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How to download all of the metadata associated with a particular EBI sample informatically?
... Here is the example of one of the samples I am interested in but there are hundreds more. https://www.ebi.ac.uk/metagenomics/samples/ERS488919 I tried using Python to scrape the HTML but it's dynamic so I'll need to try another option. **Is there any tool or method available to give a URL or s ...
next-gen sequencing written 7 weeks ago by O.rka120 • updated 7 weeks ago by genomax74k
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Where can I download the gff3 file for a specific human genome build? (hg38 release 77)
... I found this: ftp://ftp.ensembl.org/pub/release-98/gff3/homo_sapiens but there are only GTF files for release 77: ftp://ftp.ensembl.org/pub/release-77 Does anyone know where I can find this information? ...
genome assembly database written 7 weeks ago by O.rka120 • updated 7 weeks ago by Juke-342.9k
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Is there a step-by-step tutorial on creating gene models for protists? (Maker?)
... I have a diatom and I want to make gene models for this. I have the following files: (1) Repeat masked assembly; (2) RNA-seq reads; (3) RNA-seq bam files mapped to the assembly; (4) Protein homologs from other diatoms I tried running funannotate but there are so many dependencies and the pipel ...
genome assembly written 9 weeks ago by O.rka120 • updated 9 weeks ago by lakhujanivijay4.6k
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Comment: C: Segmentation fault (core dumped) when running augustus
... I posted it here b/c I wasn't getting any responses on GitHub. Do you recommend any other resources? ...
written 12 weeks ago by O.rka120
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Comment: C: Segmentation fault (core dumped) when running augustus
... I'm not sure if it's a memory issue: I ran this same command on a previous installation of `funannotate` and it worked. Here's my memory: ``` (base) -bash-4.1$ free total used free shared buffers cached Mem: 8030344 7767784 262560 0 215 ...
written 12 weeks ago by O.rka120
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(Closed) Segmentation fault (core dumped) when running augustus
... I'm using the funannotate pipeline and it fails during the augustus step. I found which command it was running and tried running it outside of funannotate and got the following error. How do I fix this? I installed on linux server via conda. augustus --stopCodonExcludedFromCDS=False --codingseq ...
augustus genome annotation written 12 weeks ago by O.rka120
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Comment: C: UK biobank HLA imputation data
... The link doesn't work to the data file. ...
written 3 months ago by O.rka120
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Comment: C: bwa mem and multiply mapped reads
... Oh ok cool, so that means both the reads would be considered mapped. Awesome, I was trying to extract the unmapped reads to figure out what was going on with my assembly. ...
written 3 months ago by O.rka120
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Comment: C: bwa mem and multiply mapped reads
... When using a tool like `reformat.sh` from BBMap, would the secondary alignments (i.e. when it maps to another spot in the genome) be included in the `unmappedonly=t` flag? ...
written 3 months ago by O.rka120

Latest awards to O.rka

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Popular Question 4 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Scholar 6 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 6 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Scholar 7 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 8 months ago, created 100 posts.
Popular Question 10 months ago, created a question with more than 1,000 views. For Is logFC in edgeR base e, 2, or 10?
Popular Question 11 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 13 months ago, created a question with more than 1,000 views. For Differential Gene Expression (EdgeR?) : What are the steps in computing this?
Scholar 13 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 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 15 months ago, created a question with more than 1,000 views. For Most up-to-date Gene Ontology [GO] analysis?
Great Question 18 months ago, created a question with more than 5,000 views. For How to tell bloodtype from SNPs data?
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 24 months 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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Popular Question 2.8 years ago, created a question with more than 1,000 views. For How to tell bloodtype from SNPs data?
Student 3.3 years ago, asked a question with at least 3 up-votes. For Most up-to-date Gene Ontology [GO] analysis?

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