updated 9 weeks ago by
Ram
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cristina_sabiers
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110
4
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45
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8
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25
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22
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40k
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6 follow
5
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22
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6.6k
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updated 10 months ago by
Ram
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50
2
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22
replies
1.3k
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6 follow
0
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21
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1.8k
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sea.joson
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9
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updated 11 weeks ago by
Ram
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written 4.8 years ago by
marongiu.luigi
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680
18
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19
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1.7k
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19
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updated 8 months ago by
Ram
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written 8 months ago by
bioinformatics
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10
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4
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120
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7
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Ram
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3.6k
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16
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3.7k
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550
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16
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10.0k
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4
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680
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10
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3.8k
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Recent Replies
Comment: BED files
by
Pierre Lindenbaum
155k
> I have been trying to solve
what did you try ? (... and your answer will contain `bedtools intersect`)
Comment: Why some insertions are symbolic in ALT column?
by
Pierre Lindenbaum
155k
shameless LLM : https://ai.tinybio.cloud/chat
> The statement "VCF is the ideal file format for genomic information; no better file format…
Comment: The .vcf format: is there a file format better suited for the era of pangenomics
by
Vincent Laufer
★
3.0k
@ram - this was as bit of a dirty tactic on my part: I stated it in the extreme to provoke disagreement. I agree with you - the irony is, d…
Comment: The .vcf format: is there a file format better suited for the era of pangenomics
by
Ram
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> .vcf is the ideal file format for genomic information; no better file format can be conceived whether in the era of singular linear refer…
Comment: GISTIC from ASCAT
by
Ram
39k
You can use pastebin or GitHub gist to paste more lines, maybe you're being restricted because you're a new user. Did GISTIC give you somet…
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
Jeremy Leipzig
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you're right it's an off-by-one-error on my part. thanks
Comment: A question about the raw RNA-seq processing workflow
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are files a,b and c all from the same sample? Or are you trying to align three different samples all together?
Comment: multiqc: group samples by population + boxplot ?
by
GenoMax
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Tagging: https://www.biostars.org/u/14100/
Rest of this line is required by biostars code.
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
Vincent Laufer
★
3.0k
@genomax thank you for clarifying that - end of an era!
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
GenoMax
130k
FYI: Emily no longer works for/at Ensembl. That is the reason she has taken out `_ensembl` from her profile.
https://www.biostars.org/u/23…
Comment: GISTIC from ASCAT
by
Hyper_Odin
▴
280
Sorry, this is how much I could paste, there is an error in the website while pasting more lines
Comment: GISTIC from ASCAT
by
Hyper_Odin
▴
280
Hi Ram, there you go
Sample Chromosome Start Position End Position Seg.CN
metastasis_H021-ARNHGQ0.47_6.segments_final.tx…
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
Vincent Laufer
★
3.0k
copy that.
also granted your background i expected nothing less :-)
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
Vincent Laufer
★
3.0k
3 quick questions:
1) are you working with a single sample or multisample VCF?
2) what genomic build? (ill assume GRCh38.p14)
3) do you…
Comment: Why does Ensembl VEP provide HGVSg for some variants and not others?
by
Jeremy Leipzig
21k
yes this should be a reproducible example using just those two lines and the latest vep and database on GRCh38
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