User: abedkurdi10
abedkurdi10 • 30
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Posts by abedkurdi10
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... You can use `cnvkit` tool to call somatic CNVs. Don't forget to use `--drop-low-coverage` argument too. ...
written 9 days ago by
abedkurdi10 • 30
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3
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Answer:
A: intersect two file
... Or You can use `dplyr` R package to do the intersection. ...
written 9 days ago by
abedkurdi10 • 30
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... It seems that there is more rRNA sequences. I downloaded `rmsk` bed file from UCSC and removed all reads covering those Repeating Elements (including and not limited to rRNA, tRNA...), then I run again `infer_experiment` and everything went well. ...
written 5 months ago by
abedkurdi10 • 30
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... I will have a look on them.
Actually, It's mouse data. ...
written 5 months ago by
abedkurdi10 • 30
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... Hello everyone,
I have received recently eight RNA-seq samples. We know that the reads are `reversely stranded`. After aligning those samples to their reference genome, I run `infer_experiment` on the alignment data just to make sure everything is fine.
Five samples out of eight showed that they ...
written 5 months ago by
abedkurdi10 • 30
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... Yes, for every gene or for genes of interest ...
written 5 months ago by
abedkurdi10 • 30
0
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1
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328
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... As I know, intervals in HaplotypeCaller are BED files (Genomic positions). You specify the regions where to call variants. ...
written 5 months ago by
abedkurdi10 • 30
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... but this is the same vcf2maf.pl which requires vep to run ...
written 6 months ago by
abedkurdi10 • 30
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... Maybe you can use `bcftools +split-vep` and extract the variants in tabulated format with specific order of the fields. ...
written 6 months ago by
abedkurdi10 • 30
1
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... While it is no more maintained, but try this: `https://github.com/cbare/vcf2maf` ...
written 6 months ago by
abedkurdi10 • 30
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3 months ago,
created a question with more than 1,000 views.
For Optimal number of samples needed to detect a variant from panel sequencing
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9 months ago,
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For raw data (fastq files) of whole exome sequencing (WES) of somatic mutations
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3.7 years ago,
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For raw data (fastq files) of whole exome sequencing (WES) of somatic mutations
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For Thresholds to filter out variants from vcf file
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For Clinical significance explanation
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For VCF file re-header
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