User: arnstrm

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arnstrm1.7k
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Posts by arnstrm

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Comment: C: Softwares for gene annotation
... Once the Maker completes, you run `fasta_merge` on the datastore to output genome level fasta (predicted proteins and transcripts), you can use the protein fasta file as input for the downstream analysis. Also, Maker also comes with other accessory scripts, where if you have annotation information ( ...
written 4 months ago by arnstrm1.7k
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Comment: C: Confusion with grep command
... Adding to what genomax said: if you're finding a list of genes using `grep`, it is always good idea to add `-F` where it evaluates the search terms as fixed strings and `-w` for whole word, so you don't bring up 10, 100, 1000 when searched with 10. ...
written 8 months ago by arnstrm1.7k
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Comment: C: Problem in execution of the commands in HMMER
... From the location where the `hmmbuild` is located, run the `pwd -P` command. Copy down the path and use that for adding to the `$PATH`. I wasn't completely sure where the `hmmbuild` in your system was located and assumed it was right! Hope this helps! ...
written 9 months ago by arnstrm1.7k
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Answer: A: Problem in execution of the commands in HMMER
... Although you installed the program, you didn't add them to PATH. PATH is like a address where the machine looks for when you call the program/executable like `hmmbuild`. One easy way to fix this is rather than calling `hmmbuild` you can provide the complete path for the executable, like `/cygwindriv ...
written 9 months ago by arnstrm1.7k
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Comment: C: slurm and CfnCluster auto-scaling
... This might be a better question for stackoverflow or other server/cloud related forums. Also, my assumption was: unless your program is mpi enabled, you can't use more than 1 node for your job, is this not right? Can you still configure so that regular program (non-mpi) can be spawned across multipl ...
written 9 months ago by arnstrm1.7k
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Job: Postdoctoral Researcher: Computational Biologist
... A postdoctoral position is available to study alterations at the microbe and animal level following application of various intervention strategies in the animal. The position will be offered through collaboration between ARS-National Animal Disease Center Food Safety and Enteric Pathogens Research U ...
postdoc jobs job research written 11 months ago by arnstrm1.7k
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Job: Senior Bioinformatician (Associate Scientist) postion at Iowa State University
... The Office of Biotechnology is seeking candidates for the position of Associate Scientist – Senior Bioinformatician. The Office of Biotechnology facilitates and advances programs in research, education, and outreach that contribute to the goals of Iowa State University’s Strategic Plan in the area o ...
jobs research academic job core bioinformatician written 11 months ago by arnstrm1.7k
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Answer: A: Enrichment Analysis from DESeq2 data
... If you have a list of genes that are deferentially expressed, you can run enrichment analysis (not just DESeq results). I use ontologizer, which is a command line tool and very easy to run. Here is how to run: 1. Before you begin, you need to have 2 important files. 1. GO ontology file, where you d ...
written 14 months ago by arnstrm1.7k
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Comment: C: BUSCOs running time
... How many threads (`-c N` or `--cpu N`) are you using? if you have large number of processors then set this accordingly, it will greatly increase the speed (default is one, I think) FYI, none of my BUSCO runs (even for genomes >2.5Gbp) ever took more than 12hrs run time (with 16 procs), but I ha ...
written 18 months ago by arnstrm1.7k
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Comment: C: Constructing HMM profile for any given aligned sequences?
... With this attitude, I'm really wondering if I should be answering this or not. Please be kind and appreciative of all the help you're getting here. (my other issues: you are not being clear about your questions, you said you did some reading, but you clearly did not: a simple glance at any amino aci ...
written 18 months ago by arnstrm1.7k

Latest awards to arnstrm

Appreciated 7 weeks ago, created a post with more than 5 votes. For A: how to unzip the files in batch?
Popular Question 4 months ago, created a question with more than 1,000 views. For PacBio coverage question for a plant genome
Appreciated 6 months ago, created a post with more than 5 votes. For A: how to unzip the files in batch?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: how to unzip the files in batch?
Great Question 7 months ago, created a question with more than 5,000 views. For Makeblastdb Error: Protein Delta Sequences Are Not Supported
Popular Question 7 months ago, created a question with more than 1,000 views. For PacBio coverage question for a plant genome
Popular Question 8 months ago, created a question with more than 1,000 views. For PacBio coverage question for a plant genome
Popular Question 9 months ago, created a question with more than 1,000 views. For PacBio coverage question for a plant genome
Great Question 15 months ago, created a question with more than 5,000 views. For SRAtoolkit: error while running fastq-dump
Appreciated 19 months ago, created a post with more than 5 votes. For A: how to unzip the files in batch?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Sample ORTHOMCL run on my Fasta file.
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Sample ORTHOMCL run on my Fasta file.
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Sample ORTHOMCL run on my Fasta file.
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: How to calculate "fold changes" in gene expression?
Popular Question 22 months ago, created a question with more than 1,000 views. For Trouble running CEGMA on the sample dataset
Popular Question 24 months ago, created a question with more than 1,000 views. For Questions about MaSuRCA assembly program
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Trouble running CEGMA on the sample dataset
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Trouble running CEGMA on the sample dataset
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Chip-Seq Visualization Without Using Any Peak Caller
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Trouble running CEGMA on the sample dataset
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Trouble running CEGMA on the sample dataset
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Trouble running CEGMA on the sample dataset
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Trouble running CEGMA on the sample dataset
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Trouble running CEGMA on the sample dataset

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