User: lait

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lait120
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Posts by lait

<prev • 63 results • page 1 of 7 • next >
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snps/indels with individual genotypes from 1000 genomes ftp site
... Sorry if this might be a trivial question! I read a lot about this until I got lost. I need to download wgs VCF file from the 1000 genomes ftp site. I need the snps (snvs and indels), most importantly, I need to have the individual genotypes of all the persons involved. so for example, this file : ...
vcf 1000 genomes genotypes ftp written 2 days ago by lait120 • updated 2 days ago by Kevin Blighe25k
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most efficient way to read from large vcf files
... Hi, if I have a large VCF file (for example, from the 1000 genomes project), what could be the most 'efficient' way (R libraries?) to extract variants from this file that lie in certain genomic regions ? The way I used to do it with small vcf files is to load them in memory and start digging, but ...
vcf written 4 days ago by lait120
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how to get genomic position from protein pdb ID+AA residue position within the protein
... Hi, We sequence trios at our lab, and we would like to check if any of the variants lie within protein-protein interaction sites. I found this database called [PiSite][1], a database for protein-protein interaction sites. For such sites, I can get the AA residues position within a protein, in addi ...
pdb protein pisite protein-protein interaction written 9 days ago by lait120
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Comment: C: is this a potential mosaicism?
... they are paired-end reads ...
written 10 days ago by lait120
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Comment: C: is this a potential mosaicism?
... Yes, we have enough genetic data for this trio and we made sure the parents are the real biological mother & father for the child ...
written 11 days ago by lait120
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Comment: C: is this a potential mosaicism?
... Thanks h.mon, please think out even louder, those are the sort of things that I need to know: how to investigate more, manually. - Please check this [image][1] , it shows the 7 reads of the mother having this mutation. - No duplicates as far as shown, or do consider the 5th and 6th reads as dupli ...
written 11 days ago by lait120
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Comment: C: is this a potential mosaicism?
... thanks for ur answer Matt. the sequencing is done for blood samples for the child, mother and father. ...
written 11 days ago by lait120
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Comment: C: is this a potential mosaicism?
... I am not sure what do you mean by PCR the DNA, I can ask our lab staff though if you give me more details. What I can say is: we always sequence our samples (WGS, illumina 2500) twice in the same run, on 2 different lanes, and then we collect the samples across different lanes. We do this to get a h ...
written 12 days ago by lait120
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Comment: C: is this a potential mosaicism?
... Sorry, there was a mistake in the AF of the mother, I just corrected it. the mother is being reported as 0/0 by varscan2, because of the low AF of 'A' that is why this mutation is considered denovo in the child So: child: 0/1, mother: 0/0, father: 0/0 ...
written 12 days ago by lait120
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is this a potential mosaicism?
... Hi, I have found a denovo mutation in the child: - coverage: 356 - Ref allele: G - Alt allele: A - ref allele: 48% (109+, 63-) - alt allele: 52% (118+, 66-) Father: - coverage: 254 - Ref allele: G - Alt allele: - - ref allele: 100% (151+, 103-) - alt allele: 0% Mother: - coverage: 211 - Ref al ...
mosaicism alignment denovo bam igv written 12 days ago by lait120

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