User: luzglongoria
luzglongoria • 40
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Posts by luzglongoria
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... Thank you so much. I think the paper you sent about the subSeq R package can help me :) ...
written 5 days ago by
luzglongoria • 40
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... It is *Plasmodium relictum* lineage GRW4. An avian malaria parasite. And yes, I have done *de novo* transcriptome assembly. ...
written 5 days ago by
luzglongoria • 40
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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
luzglongoria • 40
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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
luzglongoria • 40
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... 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
luzglongoria • 40
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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
luzglongoria • 40
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... 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 ...
written 10 days ago by
luzglongoria • 40
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... 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 ( ...
written 11 days ago by
luzglongoria • 40
• updated
11 days ago by
Emily_Ensembl ♦ 20k
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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
luzglongoria • 40
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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
luzglongoria • 40
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