User: caro-ca

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caro-ca20
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Posts by caro-ca

<prev • 76 results • page 1 of 8 • next >
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Comment: C: Is there a software that enables exploration of patterns and associations in hea
... On the other hand, I could solve the problem. I found a [link][1] to export the matrix from heatmap2. Thank you anyway. [1]: https://support.bioconductor.org/p/48624/ ...
written 5 days ago by caro-ca20
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Comment: C: Is there a software that enables exploration of patterns and associations in hea
... I made a normalized pairwise comparison of the presence and absence of a specific structural variant in thousand isolates. The challenge is to extract the clustered matrix from heatmap.2 and plot it in excel to easily know what is the sample on the x and y-axis. This is the reason why I considered u ...
written 5 days ago by caro-ca20
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Is there a software that enables exploration of patterns and associations in heatmaps?
... Dear, I want to know if there is a software that can zoom a portion of my created heatmap as I do not want to show a complete visual representation of the heatmap, instead, I would like to plot a specific region/cluster in my heatmap for an easier explanation of my data. I know there is an incredib ...
heatmap ng-chm data visualization written 5 days ago by caro-ca20
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Comment: C: Assembly convertor errors
... Great!! Thank you so much!! It worked!! ...
written 12 days ago by caro-ca20
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Assembly convertor errors
... Hi, all! I used the sacCer2 genome assembly (for S. cerevisiae) to call variants, but now I want to map the coordinates of the variants in the VCF file to another genome assembly (sacCer3). I used two web interface software: [Lift Genome Annotations][1] and [Ensembl Assembly Converter][2] Lift G ...
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Comment: C: How can I use my own genome file on Variant Effect Predictor (VEP)
... Thank you! I could run VEP with the custom genome, however, I have the feeling something is not complete as I only get intergenic variant as the major consequence of the insertions in my vcf file. This is the [output][1] obtained by running: vep -i samples_all_merged.vcf --gtf sacCer_EF2.gtf. ...
written 26 days ago by caro-ca20
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Comment: C: How can I use my own genome file on Variant Effect Predictor (VEP)
... This is the stdout while running --cache --gtf: /home/silviav/ensembl-vep/./vep -i /hosts/samples_all_merged.vcf --cache --gtf sacCer_EF2.gtf.gz --fasta Saccharomyces_cerevisiae.EF2.62.dna.toplevel.fa.gz -------------------- EXCEPTION -------------------- MSG: ERROR: Cache director ...
written 4 weeks ago by caro-ca20
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Comment: C: How can I use my own genome file on Variant Effect Predictor (VEP)
... I followed that link, but I still do not understand the argument VCF_fields. The text says "You can specify any info type (e.g. "AC")" so what kind of type is "AC"? I do not know what to add to that argument. Secondly, how could I fix the `"No format specified for custom annotation source /home/silv ...
written 4 weeks ago by caro-ca20
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Comment: C: How can I use my own genome file on Variant Effect Predictor (VEP)
... Thank you so much for your help! I downloaded the [GTF][1] and [FASTA][2] files provided in your link. Consequently I followed the steps provided ([here][3]): grep -v "#" Saccharomyces_cerevisiae.EF2.62.gtf | sort -k1,1 -k4,4n -k5,5n -t$'\t' | bgzip -c > sacCer_EF2.gtf.gz tabix sacCer_ ...
written 4 weeks ago by caro-ca20
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Comment: C: How can I use my own genome file on Variant Effect Predictor (VEP)
... Thank you for your clarification. My question was mainly because I saw VEP uses the assembly R64 or sacCer3 for Saccharomyces cerevisiae and I need the sacCer2. I found that there is the gene annotation for sacCer2 available on [Ensembl][1] , so how can I point out that the species should be Sacchar ...
written 4 weeks ago by caro-ca20

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