User: lieven.sterck

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lieven.sterck3.1k
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Posts by lieven.sterck

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Comment: C: Is is possible to use blastn to search on remote database from terminal?
... OK, yes, `blastn` is your weapon of choice then indeed. well, the DB is substantial yes, but you can download the complete DB in fasta format (and then build it locally yourself) or download the pre-formatted DB from NCBI. have a look at the ftp site of NCBI , there they offer all this ...
written 23 minutes ago by lieven.sterck3.1k
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Comment: C: Is is possible to use blastn to search on remote database from terminal?
... ok, freakish .. I was gonna comment on the fact you're using `blastn` againt the `nr` DB (=protein) , but that does seem to work ????? seems like blast is magically switching to `nt` when it notices you use `blastn` (but it's not doing so for `blastp`). It's really going downhill with the blast-pe ...
written 26 minutes ago by lieven.sterck3.1k
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Comment: C: Is is possible to use blastn to search on remote database from terminal?
... `blastn` is for DNA to DNA comparisons. `nr` is a protein DB, so either you use `nt/nr` (=the nucleotide DB) or you switch to `blastx` if you want to compare DNA to protein. It is feasible to build these DBs locally (we keep them locally in sync in our lab) but for blasting once in a while a few se ...
written 34 minutes ago by lieven.sterck3.1k
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Comment: C: How can keep the change in my fastq file when i use grep and sed to edit it?
... always start with the basics ....there is a reason why they call it 'basic' ;) once you got the hang of that, you can move on to 'advanced' stuff ...
written 3 hours ago by lieven.sterck3.1k
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Comment: C: Can Orthofinder accept whole genome data?
... I think you are having trouble with a few concepts here. - there is no easy transforming of genomic data to proteomic data. The process is called genome annotation and is not something to take lightly (your species has some influence here) - since you are taking about genes in snakes , you thus a ...
written 14 hours ago by lieven.sterck3.1k
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Comment: C: How can keep the change in my fastq file when i use grep and sed to edit it?
... simply run the `sed` command on your original file to modify it, omitting the grep part Keep in mind though that the original will then not be present anymore (as you will have changed it), a better approach might be to redirect it to a new file cat test.fastq | sed 's/@/@ILUMINA/g' > som ...
written 18 hours ago by lieven.sterck3.1k
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Comment: C: Download cdna sequences from OMA
... aha, ok, true, got your issue now. yet, if the IDs are consistent I would download the cDNA file once , blast format it and repeatedly query that one for the CDSs I need ...
written 19 hours ago by lieven.sterck3.1k
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Comment: C: Download cdna sequences from OMA
... but there is, no? cDNA Eukaryotes: Fasta format which should be all the eukaryotic cDNAs ...
written 21 hours ago by lieven.sterck3.1k
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Comment: C: Download cdna sequences from OMA
... have you looked [here][1] , there seems to be a download for all cDNA sequences [1]: https://omabrowser.org/oma/current/ ...
written 1 day ago by lieven.sterck3.1k
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Comment: C: Are there any analogs of the RAST and Prokka software for the plant transcriptom
... Interesting ... which pine species? ;) Can always have a look at [Trapid][1] , only transcript processing though [1]: http://bioinformatics.psb.ugent.be/webtools/trapid/ ...
written 2 days ago by lieven.sterck3.1k

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