User: ricardoguerreiro2121
ricardoguerreiro2121 • 20
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- Germany
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- 1 week ago
- Joined:
- 1 year ago
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Posts by ricardoguerreiro2121
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... Hi,
The accepted answer is not optimal. The entire plant database is huge and takes a long time to download via browser.
After a long time, I found the best solution:
>wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_trembl_plants.dat.g ...
written 11 days ago by
ricardoguerreiro2121 • 20
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... Hi all!
I am using an extra utility of HMMER: esl-sfetch, which retrieves parts of fastas based on asked coordinates (denoted by a -c FROM..TO) and sequence name, like this:
` esl-sfetch -c FROM..TO input.fasta sequence name`
Now, I'm finding it impossible to use FROM coordinates over 60. Bellow ...
written 4 weeks ago by
ricardoguerreiro2121 • 20
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... I would like to help, but make works with me.
This is it's output of doing make in that folder:
cc -g -c genwin.c
genwin.c: In function ‘opendbase’:
genwin.c:95:41: warning: incompatible implicit declaration of built-in function ‘strlen’ [enabled by default]
dbase->filena ...
written 10 weeks ago by
ricardoguerreiro2121 • 20
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... Hey,
I'm very new in genome annotation and am following the [tutorial][1] for maker with my own plant genome and transcriptome assemblies. I filled my maker_opts file like this:
genome=my_genassembly.fasta
est=my_RNAassembly.fasta
protein= # kept this one empty
es ...
written 10 weeks ago by
ricardoguerreiro2121 • 20
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... This guy seems to be trying it with quickmerge.
https://github.com/mahulchak/quickmerge/issues/22
It would be good to use the advantage of the 10x supernova assemblies and not just feed them as simple illumina data to another assembler...
...
written 4 months ago by
ricardoguerreiro2121 • 20
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... Thank you for the suggestion. I already had the answer I was looking for. The client wants an R script to run in windows, hehe. ...
written 9 months ago by
ricardoguerreiro2121 • 20
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... Perfect answer, thank you!
I didn't realize VCF[-c(1, 5, 7)] would subset the vcf like if it was a vector. It only prints the metainformation but when doing info(filteredVcf) you can can see that the rows are gone.
Once again thanks and have a nice day/evening! ...
written 9 months ago by
ricardoguerreiro2121 • 20
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... I know, right?? I initially did a python script and it was much easier, besides having better performance. But I need to deliver an R filter to a client that does not know (or even have installed) python... ...
written 9 months ago by
ricardoguerreiro2121 • 20
0
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... I have a filtering function that outputs desired indexes (based on, for example, the value of info(VCF)$MQ ) but I can't subscript VCF with indexes because it's not a dataframe or a vector. That is why I thought of parsing the raw lines as elements of a vector. I can just concatenate them to the hea ...
written 9 months ago by
ricardoguerreiro2121 • 20
5
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... Hello
Simple question ( I hope!)
I'm using this [VariantAnnotation][1] package from bioconductor to work with SNPs.
myparam = ScanVcfParam( # this function is a fast positional filter
samples="3441_pseudo_gatk",
which= GRanges(chr[14], # This is a chro ...
written 9 months ago by
ricardoguerreiro2121 • 20
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