User: luzglongoria

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luzglongoria40
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5 months, 4 weeks ago
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2 years, 1 month ago
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l***********@gmail.com

Posts by luzglongoria

<prev • 81 results • page 1 of 9 • next >
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Comment: C: Cytoscape and BINGO app empty output
... Thank you so much! now it works ...
written 9 months ago by luzglongoria40
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Comment: C: Cytoscape and BINGO app empty output
... I am using the EnsemblGenome name. Like for instance PF14_0329 for Mitochondrial acidic protein MAM33, putative. Is It that ok ? ...
written 9 months ago by luzglongoria40
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Cytoscape and BINGO app empty output
... Hi, It is the first time I use cytoscape and I am trying to do some Gene ontology (GO) analyses by using BINGO. I do all the steps as tutorials say. My select organism is Plasmodium falciparum and I choose the "Paste genes from text" option. Previously I have done some analyses based on RNA-seq t ...
gene bingo cytoscape rna-seq ontology written 9 months ago by luzglongoria40
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Pathway analyses with a transcriptome, which tool shall I use?
... Hi, I have a *de novo* assembly (a transccriptome) from a *Plasmodium* organism. I need to do a pathway analysis in order to determine (for instance) the enriched metabolic pathway in the transcriptome. I can compare my transcriptome with a previous genome from *Plasmodium* that has been published ...
pathway reactomepa enrichment analysis rna-seq written 10 months ago by luzglongoria40
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Comment: C: How to work with SNPs when low coverage
... Thank you so much. I think the paper you sent about the subSeq R package can help me :) ...
written 10 months ago by luzglongoria40
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Comment: C: How to work with SNPs when low coverage
... It is *Plasmodium relictum* lineage GRW4. An avian malaria parasite. And yes, I have done *de novo* transcriptome assembly. ...
written 10 months ago by luzglongoria40
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Comment: C: Working with VEP in anaconda
... I doesn't work with `--genomes` it gives the same error ...
written 10 months ago by luzglongoria40
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Comment: C: Working with VEP in anaconda
... Thanks. I have been able to run the VEP 98 version but still I have the same problem: /PATH/miniconda3/envs/salmon/ensembl-vep-98.3-0/vep -i combined.11samples.subset.freebayes.vcf -o GRW4_VEP_results.txt --species plasmodium_relictum --database --genomes Possible precedence issue wit ...
written 11 months ago by luzglongoria40
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Comment: C: How to work with SNPs when low coverage
... Thank you so much for your response. I have already done some analysis and get a .vcf file with the calling of variants. Shall I compare this data with full-coverage dataset? And how can I do that? ...
written 11 months ago by luzglongoria40
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Comment: C: Working with VEP in anaconda
... Thank you so much. Following the instructions I have upload the cache file to where ./vep is installed and then run the command tar xzf plasmodium_relictum_gca_900005765_vep_45_PRELSG.tar.gz after that I have tried to run the command for VEP as usual but I get the error : vep -i combined ...
written 11 months ago by luzglongoria40

Latest awards to luzglongoria

Scholar 8 months ago, created an answer that has been accepted. For A: Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array exte
Great Question 10 months ago, created a question with more than 5,000 views. For Error in dimnames(x) <- dn : length of 'dimnames' [1] not equal to array extent
Popular Question 10 months ago, created a question with more than 1,000 views. For How to combine two .sam files?
Popular Question 11 months ago, created a question with more than 1,000 views. For Encountered internal Bowtie 2 exception (#1) bowtie2-align exited with value 1
Popular Question 12 months ago, created a question with more than 1,000 views. For Encountered internal Bowtie 2 exception (#1) bowtie2-align exited with value 1
Popular Question 15 months ago, created a question with more than 1,000 views. For How to combine two .sam files?
Popular Question 16 months ago, created a question with more than 1,000 views. For Encountered internal Bowtie 2 exception (#1) bowtie2-align exited with value 1
Popular Question 17 months ago, created a question with more than 1,000 views. For How to combine two .sam files?
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Popular Question 20 months ago, created a question with more than 1,000 views. For How to combine two .sam files?

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