mcscanx
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7 weeks ago

I have made files as per given in example blast and gff file

xyz.blast contains: Eg01_t003090.1 Eg01_t003090.1 100.00 306 0 0 1 306 1 306 5e-173 594 Eg01_t003090.1 Eg01_t003100.1 98.38 309 2 1 1 306 1 309 1e-171 590 Eg01_t003090.1 Mba03_g02610.1 93.46 306 19 1 1 306 1 305 1e-163 563 Eg01_t003090.1 Mba03_g02600.1 93.46 306 19 1 1 306 1 305 2e-163 562 Eg01_t003090.1 Macma4_03_g02690.1 90.55 307 27 2 1 306 1 306 3e-161 555 Eg01_t003100.1 Eg01_t003100.1 100.00 309 0 0 1 309 1 309 5e-175 601

xyz.gff contains: chr01 Eg01_t003090.1 2241205 2242304 chr01 Eg01_t003090.1 2241205 2242304 chr01 Eg01_t003090.1 2241205 2241796 chr01 Eg01_t003090.1 2241889 2242115 chr01 Eg01_t003090.1 2242203 2242304 chr01 Eg01_t003090.1 2241205 2241796 chr01 Eg01_t003090.1 2241889 2242115

I am getting -

xyz.collinearity as:

<h6>######### Statistics</h6>

Number of collinear genes: 0, Percentage: 0.00

Number of all genes: 74

xyz.tandem as: Eg01_t003100.1,Eg01_t003090.1 Mba01_g21150.1,Eg01_t028010.1 Eg05_t008600.1,Mba05_g08270.1 Eg07_t003220.1,Mba07_g18470.1 Eg08_t044500.1,Eg08_t044540.1

Why there is no alignment output in collinearity file

duplication synteny • 242 views
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I think you'll need to provide much more context regarding your approach and aims, and reformat your question for legibility

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May I know how to prepare blast file for MCScanx what format do I need to use. I compared with sample file all files are as per examples still I didn't get proper output

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