User: Jon

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Jon340
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Posts by Jon

<prev • 33 results • page 1 of 4 • next >
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Comment: C: What is required for genome annotation?
... You can use Funannotate - it is flexible on input requirements, only thing necessary is an assembly. Docs are here: [http://funannotate.readthedocs.io/en/latest/][1]. Github here: [https://github.com/nextgenusfs/funannotate][2] [1]: http://funannotate.readthedocs.io/en/latest/ [2]: https://git ...
written 24 months ago by Jon340
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Comment: C: bash: tophat: command not found
... I know not part of your question, but TopHat is deprecated and even the developers have [told people to stop using it][1]. Their replacement aligner is called [hisat2][2]. [1]: https://twitter.com/lpachter/status/937055346987712512?lang=en [2]: https://ccb.jhu.edu/software/hisat2/index.shtml ...
written 2.6 years ago by Jon340
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Answer: A: proteinOrtho out put help required
... You need to parse the file tab delimited file named .proteinortho or .poff (if you used syteny). Per the [manual][1], you'll see that the first column is the number of species that the orthologous group is found in. So lets say you had 4 species (i.e. you ran with 4 proteome fasta files), you could ...
written 2.6 years ago by Jon340
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Comment: C: Metagenomics with non-overlapping pairs
... I'm not familiar with FLASH, but if they are amplicon data you could merge with usearch or vsearch and capture the unmerged forward reads, concatenate them with merged reads (trim primers?), then use vsearch to dereplicate (remove duplicates), which should get you down to a much smaller number of se ...
written 2.6 years ago by Jon340
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Comment: C: Command to estimate how long local blastx take to finish the job?
... You might be able to use `pv`, i've not used it, but seems like it may be able to give you a progress bar and estimate of completion. [https://github.com/icetee/pv][1]. [1]: https://github.com/icetee/pv ...
written 3.2 years ago by Jon340
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Comment: C: counting the reads mapped to specific coordinate in the genome
... You can likely use your tRNA annotations (if GFF format) directly with several tools, otherwise convert to BED format which you should be able to use as intervals. Counting the reads can be done with several tools ...
written 3.2 years ago by Jon340
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Comment: C: Eukaryotic Genome Annotation in 2016
... From discussions with Brian Haas, the evidences are somewhat empirical. Meaning that it depends a lot on what the input data is. Depending on the evidence that you pass to funannotate, the scripts automatically go with recommendations close to what Brian has recommended. Which are: in silico pred ...
written 3.2 years ago by Jon340
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Comment: C: Eukaryotic Genome Annotation in 2016
... For protein evidence alignments to a genome, you want to use exonerate --model protein2genome. Exonerate does a good job, but is pretty slow. What I do in funannotate is to run tblastn to get hits and then slice the genome according to hit location and run exonerate on that section - this speeds u ...
written 3.4 years ago by Jon340
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Comment: C: Eukaryotic Genome Annotation in 2016
... The more relevant evidence you can use the better. I routinely use EST clusters from closely related species in my funannotate pipeline and then use curated UniProtKB proteins as evidence. I would try to use transcripts that are actually experimental, i.e. using the annotation from a closely relat ...
written 3.4 years ago by Jon340
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Comment: C: parsing only 100% identical hits out of BLAST tab
... Yes, but the reason is because it is doing local alignment.... global alignment does exactly that compares across the entire sequence. ...
written 3.4 years ago by Jon340

Latest awards to Jon

Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Augustus install mac
Good Answer 24 months ago, created an answer that was upvoted at least 5 times. For A: Eukaryotic Genome Annotation in 2016
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Biopython SeqIO: remove gene annotation if not in a list from GenBank file
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: bash: tophat: command not found
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Biopython SearchIO HMMer 3 parsing, HMM model length?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Eukaryotic Genome Annotation in 2016
Appreciated 3.7 years ago, created a post with more than 5 votes. For A: Eukaryotic Genome Annotation in 2016
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Eukaryotic Genome Annotation in 2016
Scholar 4.7 years ago, created an answer that has been accepted. For A: How to obtain and compare genomic coordinates from RepeatMasker output?

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