User: john.anderson.ivy

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Posts by john.anderson.ivy

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Comment: C: parsing Affymetrix file
... I don't understand how this is possible. In this case why all the genotypes contain two letters ( in my above example AA or TC ) instead of one? ...
written 6 weeks ago by john.anderson.ivy10
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Comment: C: parsing Affymetrix file
... The problem I have is that some SNPs in the same files on different rows have different genotype so I don;t know which one is the correct Genotype probeset_id CEL_call_code chromosome position rsid AX-96108113 AC 4 6301295 rs1801214 AX-96108115 ...
written 6 weeks ago by john.anderson.ivy10
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Comment: C: parsing Affymetrix file
... I need to transform the file from this format probeset_id CEL_call_code chromosome position rsid AFFX-SP-000001 CC 10 121336954 rs10466213 AFFX-SP-000002 CG 12 23048418 rs10770943 AFFX-SP-000004 GG 17 ...
written 6 weeks ago by john.anderson.ivy10
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Comment: C: parsing Affymetrix file
... How do I found out which array version it is? What I need to do is to make a script to extract the corect SNP and their genotype. Because same SNPs have different call code I don't know how I can chose which one is the corect one. You mentioned normalization, but this file shouldn't be already nor ...
written 6 weeks ago by john.anderson.ivy10
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parsing Affymetrix file
... I need some help understanding the structure of a variant call file, with Affymetrix data I have a RAW data file in the following format: probeset_id CEL_call_code chromosome position rsid AFFX-SP-000001 CC 10 121336954 rs10466213 AFFX-SP-000002 CG ...
assembly sequence snp written 6 weeks ago by john.anderson.ivy10
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Question converting different genetic file formats into another file
... Hi, can anyone provde a ppt/pdf/link to a tutorial which can give you detailed information of how to convert any genetic file (BAM, SAM, VCF, FASTQ, FASTA, etc.) in another genetic file format? I am interested in tools and documentation of how to do this in house. Any expert help would be much app ...
genome assembly alignment written 9 weeks ago by john.anderson.ivy10 • updated 9 weeks ago by Biostar ♦♦ 20

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