User: gmora

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gmora20
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Posts by gmora

<prev • 7 results • page 1 of 1 • next >
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Comment: C: How to find the mapping quality (mapQ) score of a variant
... Thanks for your reply, Istvan "What you could do however is examine the MAPQ of the alignments that do overlap with your variants and tabulate the MAPQ for these alignments. See if there is a pattern to them." This is exactly what I want to accomplish. I am unsure how to go from the variant and det ...
written 2.3 years ago by gmora20
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Comment: C: How to find the mapping quality (mapQ) score of a variant
... Thank you for the reply Pierre, I am curious if during the alignment process there are two regions that are highly similar say a gene and it's known pseudogene. My theory is that if I examined the MAPQ scores for these reads, I would be able to determine if the read was originating from the gene or ...
written 2.3 years ago by gmora20
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How to find the mapping quality (mapQ) score of a variant
... Given you have a SAM file and VCF file, is it possible to determine the mapQ score(s) for a particular variant? The overarching goal is to determine if a variant is a false positive because of non-unique mapping. Thanks in advance. ...
vcf sam written 2.3 years ago by gmora20 • updated 2.3 years ago by Lauren50
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protein structure from gene variant in FLNA gene
... I have a variant in a gene that has been linked to a phenotype. However this gene is associated with a number of different phenotype based on where a mutation lies in this gene; that is variants in the early exons 2-10 may cause cardiac issues, similarly variants in exons 22-25 have neuron migration ...
gene protein pymol written 3.4 years ago by gmora20
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Answer: C: Ensembl VEP cannot parse HGVS notation.
... Solved it appears as though the ENST transcript have slightly different naming conventions for variants in the UTR regions. ...
written 3.5 years ago by gmora20
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Ensembl VEP cannot parse HGVS notation.
... Hello. So I used VEP to analyze ENST to refseq transcripts in terms of position differences between them. However when I run my HGVS notations through VEP I get these errors (for HBA1 gene, if that helps). WARNING: Unable to parse HGVS notation 'ENST00000320868:c.-52C>T' WARNING: Unable to par ...
hgvs ensembl vep ref_seq parsing written 3.5 years ago by gmora20 • updated 14 months ago by zx87548.4k
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Conversion tool from ENST(ensembl) transcript to NM transcript(NCBI)
... So I have hundreds ensemble gene transcripts which needs to be converted to NCBI transcripts. I am worried about their being position changes in known mutations. I think one of reasons for this change is to have consecutive exons numbering (1,2,3 etc) instead of (1b,2,3,5) that is found in ensembl. ...
ncbi ensembl transcript conversion written 3.5 years ago by gmora20 • updated 23 months ago by Biostar ♦♦ 20

Latest awards to gmora

Popular Question 17 months ago, created a question with more than 1,000 views. For How to find the mapping quality (mapQ) score of a variant
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Conversion tool from ENST(ensembl) transcript to NM transcript(NCBI)

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