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Using 2.3.2 installed via conda with samtools 1.5 I get the following error after deduping:
```
2017-09-01 16:39:09,002 [ INFO] - Deduplicating NuGEN paired end reads...
2017-09-01 16:39:09,4…
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What Python environment are you using? I tried versions 3.6 to 3.9, but I couldn't run the code 'python main.py compute-order-aware-alignments -p -l Bpic12.xes -m Bpic12_90.pnml'. Moreover, the compi…
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I think @jablazek is particularly interested in this idea.
general trend should be that less elliptical haloes display less alignment with central galaxies.
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-a means output all alignments for SE or unpaired PE, I find there is a bug
two different ref, first is only a genome A, but second is thousands genomes including A, some reads can map first ,but can…
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```
The reason for this is limited by the size of exact hit, which was 199 in
version of 0.2.9.4 or before. In 0.2.9.4, you can enlarge the number of matches
by using -k 1000, which allow 1000 align…
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Great software!
Is there a way to retrieve the alignments as plaintext FASTAs other than retrieving them from the html output?
Thanks!
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```
But a general approach for complex superposition? Without alignments given:
first do all-against-all superposition within one complex to get symmetry
classes
then to the same for the other co…
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Sometimes refinement algorithms converge into the same solution but with different handedness. Both solutions are correct. However, align volume and particles does not consider this and produces incor…
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When I run RetroSeq in the align mode, it gets to PE alignment parsing and then breaks. Not sure what the error means (uninitialized value before assignment?).
Input: perl bin/retroseq.pl -discover -…
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Hello!
I was wondering if `methylpy` methylation calling takes care of directional and non-directional libraries? To quote Bismark User guide here
> Bisulfite treatment of DNA and subsequent PCR…