User: abedkurdi10
abedkurdi10 • 30
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Posts by abedkurdi10
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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 6 weeks ago by
abedkurdi10 • 30
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... I will have a look on them.
Actually, It's mouse data. ...
written 6 weeks 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 6 weeks ago by
abedkurdi10 • 30
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... Yes, for every gene or for genes of interest ...
written 8 weeks ago by
abedkurdi10 • 30
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... As I know, intervals in HaplotypeCaller are BED files (Genomic positions). You specify the regions where to call variants. ...
written 9 weeks ago by
abedkurdi10 • 30
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... but this is the same vcf2maf.pl which requires vep to run ...
written 11 weeks 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 11 weeks ago by
abedkurdi10 • 30
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... While it is no more maintained, but try this: `https://github.com/cbare/vcf2maf` ...
written 11 weeks ago by
abedkurdi10 • 30
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Comment:
C: Bigwig circular plot
... Thank you for your suggestion.
Actually, I am looking for interactive plots rather than static ones, like zooming in and out, moving tracks... ...
written 3 months ago by
abedkurdi10 • 30
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... Hello all,
Does anyone knows about representing BigWig in a circular plot? Any tool or library especially in JavaScript that can be used to represent BigWig files?
I appreciate the suggestions,
Thank you ...
written 4 months ago by
abedkurdi10 • 30
• updated
4 months ago by
Pierre Lindenbaum ♦ 129k
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