User: Charlie2

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Charlie230
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1 year, 1 month ago
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Posts by Charlie2

<prev • 18 results • page 1 of 2 • next >
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Comment: C: REF and ALT alleles seem to be wrong way round in dbSNP
... Ah, thanks, still learning how it all works. I *think* I've marked it as solved now. ...
written 3 months ago by Charlie230
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Comment: C: REF and ALT alleles seem to be wrong way round in dbSNP
... Thank you, that's really helpful. ...
written 3 months ago by Charlie230
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Comment: C: REF and ALT alleles seem to be wrong way round in dbSNP
... Ah, thank you - I'm very new to all this and get confused with the terminology. ...
written 3 months ago by Charlie230
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REF and ALT alleles seem to be wrong way round in dbSNP
... This is probably a *really* stupid newbie question, but I'm looking at [rs1529927][1] in dbSNP and confused to see that although it gives the Alleles as: Alleles C>G it then gives Frequency as: Frequency C=0.02066 (2594/125568, TOPMED) C=0.02443 (2966/121398, ExAC) ...
dbsnp snp written 3 months ago by Charlie230
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Comment: C: Could you help me set up a VCF filter?
... Ah, sorry, I didn't realise that would cause difficulties. The GRCh38 VCFs I've already got include the LongRanger files and also a few others from a different pipeline (possibly GATK?), but I think he did do some things slightly differently from usual to work better with the chromium data. Yes, i ...
written 9 months ago by Charlie230
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Comment: C: Could you help me set up a VCF filter?
... Hello again, one more quick question before I open the new post: I've run bamtofastq with just the default command - would it be worth running it again with any of the options, e.g. -fq2? My sequence is from chromium 10x linked read. Thanks again for your help. ...
written 9 months ago by Charlie230
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Comment: C: Could you help me set up a VCF filter?
... Thank you, that's really helpful. I'm just working out how to use bamtofastq then will open a new question as you suggest. I *will* get there! ...
written 9 months ago by Charlie230
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Comment: C: Could you help me set up a VCF filter?
... Lol it had occurred to me that if I really couldn't get anywhere I might have to resort to excel, but it'd be a very long, tedious, error-prone process. I haven't explained very well, but the initial couple of genes are only the first step. Even if I do have clear evidence of the most strongly indic ...
written 9 months ago by Charlie230
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Comment: C: Could you help me set up a VCF filter?
... I actually already have the BAM file so it'd be great if you could show me how to re-align from that. Re interpretation, my plan was to first see if I have any of the known pathogenic mutations in the genes most strongly implicated by the clinical presentation. There is a fairly strong suspicion of ...
written 9 months ago by Charlie230
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Comment: A: Could you help me set up a VCF filter?
... Hi, thank you and sorry for slow reply - I'm not well and can't always use the computer. I said either liftover or realign because I thought you had said it might be possible to take it back to fastq and align to GRCh37 myself, if my computer could handle it. I may well have misunderstood that thou ...
written 9 months ago by Charlie230

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