User: luzglongoria

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luzglongoria40
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3 hours ago
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1 year, 3 months ago
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Posts by luzglongoria

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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 5 days 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 5 days 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 5 days 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 10 days 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 10 days 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 10 days ago by luzglongoria40
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How to work with SNPs when low coverage
... Hi there, I am working with RNA-seq of a organism (*Plasmodium*) that does not have reference genome. Which is readily available is a genome of a very related species. So I willl use the reads and the reference genome for determining the SNPs and differences between these two species. The problem I ...
rna-seq snp coverage written 10 days ago by luzglongoria40
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Working with VEP in anaconda
... Hi there, I'm working on a project for determining how this two protozoan organisms have evolved and in which genes they differ the most by looking at the SPNs. I have done some previous analysis calling for variants by using some programs # construct the FM-index for the reference genome ( ...
anaconda vep conda snp rna-seq written 11 days ago by luzglongoria40 • updated 11 days ago by Emily_Ensembl20k
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Comment: C: Segmentation fault Freebayes
... I run it and after 5 seconds it dies... About the memory df -h System load: 4.56 Local Users: 7 Memory usage: 0.0% System uptime: 54 days Usage on /home: 73% Swap usage: 0.0% Filesystem Size Used Avail Use% Mounted on /dev/ma ...
written 20 days ago by luzglongoria40
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Comment: C: Segmentation fault Freebayes
... It is the first time I run freebayes. I am running in a local server (not in my computer) which is shared. I know some other collegues have run freebayes on it properly. May be is a problem of the size of my samples? ...
written 20 days ago by luzglongoria40

Latest awards to luzglongoria

Popular Question 10 days 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 7 weeks 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 5 months ago, created a question with more than 1,000 views. For How to combine two .sam files?
Popular Question 5 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 6 months ago, created a question with more than 1,000 views. For How to combine two .sam files?
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Popular Question 10 months ago, created a question with more than 1,000 views. For How to combine two .sam files?

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