Question

Affymetrix microarrays parsing

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7.2 years ago

Sebastian ▴ 20

I am working with Affymetrix microarrays.

I need to parse the the output txt file into snp:allele pairs.

Which will be the best tool

Affymetrix microarrays • 1.2k views

ADD COMMENT • link 7.2 years ago by Sebastian ▴ 20

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Exactly which fields of the txt file you need to extract?

ADD REPLY • link 7.2 years ago by veronicaschroeder78 ▴ 140

score 0 · Answer 1 · 2017-03-15

I have file like this

probeset_id DG_2017022201_A09_41001606050490.CEL_call_code DG_2017022201_A10_41001606050518.CEL_call_code DG_2017022201_A11_41001606050505.CEL_call_code DG_2017022201_A12_41001606050180.CEL_call_code DG_2017022201_B09_41001606050231.CEL_call_code DG_2017022201_B10_41001606050120.CEL_call_code DG_2017022201_B11_41001606050358.CEL_call_code DG_2017022201_B12_41001606050463.CEL_call_code DG_2017022201_C09_41001606050478.CEL_call_code DG_2017022201_C10_410016060500404.CEL_call_code DG_2017022201_C11_41001606050390.CEL_call_code DG_2017022201_C12_41001606050416.CEL_call_code DG_2017022201_D09_41001606050459.CEL_call_code DG_2017022201_D10_41001606050497.CEL_call_code DG_2017022201_D11_41001606050155.CEL_call_code DG_2017022201_D12_41001606050193.CEL_call_code DG_2017022201_E09_41001606050298.CEL_call_code DG_2017022201_E10_41001606050197.CEL_call_code DG_2017022201_E11_41001606050129.CEL_call_code DG_2017022201_E12_410011606050136.CEL_call_code DG_2017022201_F09_41001606050371.CEL_call_code DG_2017022201_F10_41001606050196.CEL_call_code DG_2017022201_F11_41001606050312.CEL_call_code DG_2017022201_G09_41001606050206.CEL_call_code DG_2017022201_G10_41001606050199.CEL_call_code DG_2017022201_G11_41001606050247.CEL_call_code DG_2017022201_H09_41001606050448.CEL_call_code DG_2017022201_H10_41001606050487.CEL_call_code DG_2017022201_H11_41001606050205.CEL_call_code dbSNP_RS_ID AX-100002678 CC CC TC CC CC CC CC CC CC CC CC CC TC TC CC CC CC CC TC CC CC CC CC TC TC CC CC CC CC rs7072122 AX-100002700 CC CC CC --- CC CC CC TC TC TC TC TC CC TC CC TC TC CC CC CC CC CC CC TC CC TC CC CC CC rs12570744 AX-100002725 TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT TT rs11188352

I need to convert to snp file