User: ricardoguerreiro2121

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Posts by ricardoguerreiro2121

<prev • 17 results • page 1 of 2 • next >
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Answer: A: how to get database of plants in FASTA format from uniprot
... 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 ricardoguerreiro212120
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HMMER esl-fetch corrupt coords
... 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 ...
hhmer esl written 4 weeks ago by ricardoguerreiro212120
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Answer: A: Alternatives to RepeatModeler / nseg install fail
... 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 ricardoguerreiro212120
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Maker (Gene annotation) RepeatMasker error
... 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 ...
gene annotation repeatmasker maker written 10 weeks ago by ricardoguerreiro212120
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Answer: A: pacbio-illumina hybrid assemblies
... 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 ricardoguerreiro212120
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Comment: C: Parse raw vcf in R from CollapsedVCF (VariantAnnotation library)
... 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 ricardoguerreiro212120
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Comment: C: Parse raw vcf in R from CollapsedVCF (VariantAnnotation library)
... 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 ricardoguerreiro212120
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Comment: C: Parse raw vcf in R from CollapsedVCF (VariantAnnotation library)
... 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 ricardoguerreiro212120
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Comment: C: Parse raw vcf in R from CollapsedVCF (VariantAnnotation library)
... 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 ricardoguerreiro212120
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Parse raw vcf in R from CollapsedVCF (VariantAnnotation library)
... 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 ...
vcf bioconductor variantannotation written 9 months ago by ricardoguerreiro212120

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Supporter 9 months ago, voted at least 25 times.

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