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BISulfite-seq CUI Toolkit
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Weird rectangle output #44

Open weishwu opened 3 years ago

weishwu commented 3 years ago

If I run rectangle directly on my epiread it says: "[main_rectangle:79] Error, rectangle cannot cross chromosomes". The manual does not say the input has to be chromosome split. If I run it on a subset of the epiread in chr1, it finishes but the output looks weird. The output simply appends a 9th column to the epiread file and the 9th column is a string of 1,020,893 Ns.

My epiread input:

1   K00135:125:HFV57BBXX:1:1223:20618:2404  2   -   39154135    C   .   .
1   K00135:125:HFV57BBXX:1:1223:20618:2404  1   -   39154135    C   .   .
1   K00135:125:HFV57BBXX:3:2211:8044:44482  1   +   47760131    C   .   .
1   K00135:125:HFV57BBXX:1:2212:23673:26898 1   -   61731684    CCC .   .
1   K00135:125:HFV57BBXX:1:2212:23673:26898 2   -   61731684    CCC .   .
1   K00135:125:HFV57BBXX:1:2109:1702:26318  1   -   69191536    TTTCCCC .   .
1   K00135:125:HFV57BBXX:3:1109:11759:18599 2   -   173991209   C   .   .
1   K00135:125:HFV57BBXX:3:1109:11759:18599 1   -   173991209   C   .   .

My rectangle command-line:

biscuit_0_3_16_linux_amd64 rectangle -o epiread_rslM1Li_chr1_epiread_matrix Mus_musculus.GRCm38.dna_sm.primary_assembly.fa epiread_rslM1Li_chr1.epiread