User: Tania

gravatar for Tania
Tania120
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9 months, 2 weeks ago
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Posts by Tania

<prev • 135 results • page 1 of 14 • next >
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Check CNV analysis from CNVnator
... **Hi every one** I used CNVnator to get a CNV list for each patient sample using exome (not sure if ok) and whole genome whatever I have. I pick those with ev2 <0.05 from CNVnator. Then I use the genome browser to find the genes that map to these CNVs intervals, and also find out if these C ...
exome whole genome cnv written 6 days ago by Tania120
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Comment: C: How to remove duplicate SNPs from plink ped,vcf?
... thanks Kevin so much. I will follow the links you mentioned and see. Thanks so much. ...
written 10 weeks ago by Tania120
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Comment: C: How to remove duplicate SNPs from plink ped,vcf?
... No worries :) Thanks alot for helping me :) This is a snp-array handled to me few days ago, for some patients. I have to find out the reason for the phenotype they have. So I am trying to get a vcf then go from here. Each of these codes Spxxx , Fxxx is a patient, so I really don't know why they ...
written 10 weeks ago by Tania120
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Comment: C: How to remove duplicate SNPs from plink ped,vcf?
... Thanks Kevin. I have many smaples duplicated like this. How can I understand the reason of duplication? Is it something to check with the data generation itself? or something computational I look to find? Sorry,seems naiive, but I am new here completely :) ...
written 10 weeks ago by Tania120
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How to remove duplicate SNPs from plink ped,vcf?
... **Hi Every one** I used to get this error when I try to split a vcf I get from plink format: > [E::bcf_hdr_add_sample] Duplicated sample name '103_Sp676' **These are my steps to remove duplicates, however I still get the same error:** data.bed: plink --file data --maf 0. ...
plink snp written 10 weeks ago by Tania120 • updated 10 weeks ago by Kevin Blighe26k
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Comment: C: Does high or low GC content affect base quality?
... Thanks Kevin, that's a nice explanation too :) ...
written 12 weeks ago by Tania120
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Comment: C: Does high or low GC content affect base quality?
... great, thanks genomax. Was just checking it worth sanger sequencing not to simply throw it away :) ...
written 12 weeks ago by Tania120
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Comment: C: Does high or low GC content affect base quality?
... Thanks Kevin a lot :) so my final point here does it worth Sanger sequencing? Like the variant exist in all affected patients, the low quality is in only one patient, lets say patient X. All other affected people have the variant with high mapping and quality. If we ignore the variant in patient x ...
written 12 weeks ago by Tania120
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Comment: C: Does high or low GC content affect base quality?
... No, I have a variant with very low GC content. Found in all affected except one person. This person all reads agree with the reference but all bases are as low as 5 and mapping quality is also below 20. So was thinking does this low GC content could make terrible bases? Should I proceed to verify w ...
written 12 weeks ago by Tania120
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Does high or low GC content affect base quality?
... Hi everyone I understand that high or low GC content affect coverage, but could high or low GC content affect bases' quality too? And is there difficulty proving a variant by Sanger sequencing if it is in a high or low GC content? Thanks ...
rna-seq written 12 weeks ago by Tania120

Latest awards to Tania

Centurion 5 months ago, created 100 posts.
Student 5 months ago, asked a question with at least 3 up-votes. For Is there a better tool for visualizing your variants after annotation than Excel?
Supporter 8 months ago, voted at least 25 times.
Rising Star 8 months ago, created 50 posts within first three months of joining.

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