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The output is different from the example result #15

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Cp0728 opened this issue Aug 20, 2024 · 1 comment
Open

The output is different from the example result #15

Cp0728 opened this issue Aug 20, 2024 · 1 comment

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@Cp0728
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Cp0728 commented Aug 20, 2024

Region Position Reference Strand Coverage-q30 MeanQ BaseCount[A,C,G,T] AllSubs Frequency gCoverage-q30 gMeanQ gBaseCount[A,C,G,T] gAllSubs gFrequency
chr21 31744050 C 2 4 37.75 [0, 3, 0, 1] CT 0.25 - - - - -
chr21 40765196 T 2 14 35.79 [0, 1, 0, 13] TC 0.07 - - - - -
chr21 40768815 A 2 12 37.83 [8, 4, 0, 0] AC 0.33 - - - - -
chr21 40768841 T 2 9 37.89 [0, 4, 0, 5] TC 0.44 - - - - -
chr21 40768844 T 2 9 37.56 [0, 1, 0, 8] TC 0.11 - - - - -
chr21 40769017 G 2 4 37.75 [0, 0, 2, 2] GT 0.50 - - - - -
chr21 40769264 T 2 16 37.94 [0, 1, 0, 15] TC 0.06 - - - - -
chr21 40769290 A 2 16 37.94 [13, 0, 3, 0] AG 0.19 - - - - -
chr21 40769447 T 2 17 37.24 [0, 1, 0, 16] TC 0.06 - - - - -
chr21 45732074 C 2 18 37.78 [0, 17, 0, 1] CT 0.06 - - - - -
chr21 45732102 G 2 17 37.29 [2, 0, 15, 0] GA 0.12 - - - - -
chr21 45732115 T 2 13 36.92 [0, 1, 0, 12] TC 0.08 - - - - -
chr21 45732116 C 2 16 37.31 [0, 3, 0, 13] CT 0.81 - - - - -
chr21 45732128 C 2 16 37.06 [0, 15, 0, 1] CT 0.06 - - - - -
chr21 45732902 A 2 15 37.53 [14, 0, 1, 0] AG 0.07 - - - - -
chr21 47545210 A 2 33 37.24 [32, 1, 0, 0] AC 0.03 - - - - -
chr21 47545212 C 2 33 37.73 [0, 32, 0, 1] CT 0.03 - - - - -
chr21 47545381 T 2 31 37.23 [1, 0, 0, 30] TA 0.03 - - - - -
chr21 47545395 T 2 31 37.45 [0, 1, 0, 30] TC 0.03 - - - - -
chr21 47545411 G 2 60 37.23 [2, 0, 58, 0] GA 0.03 - - - - -
chr21 47545416 C 2 60 37.47 [0, 58, 0, 2] CT 0.03 - - - - -
chr21 47545424 A 2 32 37.25 [31, 0, 1, 0] AG 0.03 - - - - -
chr21 47545435 A 2 30 37.30 [29, 0, 1, 0] AG 0.03 - - - - -
chr21 47545465 A 2 64 37.47 [63, 0, 0, 1] AT 0.02 - - - - -

I use REDITools2.0.This is the result of the .bam output using the example data SRR2135332 after I configure the environment, only chromosome 21 is output, why is it inconsistent with the result on the picture shown, I would like to ask if the data of chromosome 21 shown is SRR2135332.bam? Or is there a problem with my environment configuration?

@Cp0728
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Cp0728 commented Aug 20, 2024

python src/cineca/reditools.py -f test/SRR2135332.bam -r test/chr21.fa -g chr21 -o test/serial_table.txt -S

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