PacificBiosciences kineticsTools issues

PacificBiosciences / kineticsTools

Tools for detecting DNA modifications from single molecule, real-time sequencing data

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issues

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ipdSummary for Revio data

#101 jxmelody opened 1 month ago
0
Any detailed description of the input files for summarizeModifications softwares

#100 Jingquan-Li opened 4 months ago
1
The results are mapped to an opposite strand than their alignment, does the argument --referenceWindow remains the same for both strands?

#99 Marjan-Hosseini opened 5 months ago
0
How critical is the "Non-unique read group integer IDs found" warning in running ipdSummary?

#98 Marjan-Hosseini opened 6 months ago
3
ipdSummary command stops working if --identify m5C_TET is included in command, and does not give any m5C info either

#97 Marjan-Hosseini opened 6 months ago
1
ipdSummary takes significant time but at a low CPU use

#96 ck-theory opened 1 year ago
0
ipdSummary -- KeyError: "tag 'ip' not present"

#95 ck-theory closed 1 year ago
2
ValueError: invalid literal for int() with base 16: 'myid'

#94 tongyin121 closed 2 years ago
0
Release on PyPI?

#93 palao opened 2 years ago
1
ipdSummary: AssertionError Child process exited with exitcode=1

#92 anikajohn opened 2 years ago
1
Is replaceScipyNormPdf in MixtureEstimationMethods.py correct?

#91 ZhangBio opened 2 years ago
0
Child process exited with exitcode=1. Aborting.

#90 GaoChengyu opened 2 years ago
1
Support HDF5 outputs again

#89 hisakatha opened 2 years ago
1
the output content does not increase in one place

#88 chenchen-eng opened 2 years ago
0
the data set for model training

#87 SarahChen0401 opened 3 years ago
3
Stop at the same region of genome

#86 DustinChen1986 opened 3 years ago
1
Is there any oringinal papers of kineticsTools?

#85 huiiuaa opened 3 years ago
0
[Feature request] Verified versions in GitHub

#84 GDelevoye opened 3 years ago
0
Installing kineticsTools

#83 venkata14 closed 3 years ago
4
[ERROR] [root monitorChildProcesses 593] Child process exited with exitcode=-9. Aborting.

#82 SarahChen0401 closed 3 years ago
3
Is there a mistake in script MixtureEstimationMethods.py?

#81 xyw1 opened 3 years ago
1
ipdSummary: Chemistry cannot be identified---cannot perform kinetic analysis

#80 wxie-18 opened 3 years ago
2
Running ipdSummary faster？

#79 chenzixi07 closed 3 years ago
4
KeyError: 'Ipd'

#78 nick-youngblut closed 4 years ago
3
ipdSummary: UnboundLocalError: local variable 'mods' referenced before assignment

#77 nick-youngblut opened 4 years ago
5
Use Python3 in test

#76 emollier opened 4 years ago
0
testShared.py: Fix import statement for tests

#75 emollier opened 4 years ago
0
Align columns of the first tabular

#74 emollier opened 4 years ago
0
Two small typos in manual.rst

#73 smoe opened 4 years ago
0
build failure: pbcommand no longer offers pbparser_runner

#72 smoe closed 4 years ago
2
Update README.md

#71 GDelevoye closed 3 years ago
3
ImportError: No module named pyBigWig

#70 liufeibio opened 4 years ago
9
Training sets for GBM learning machinery

#69 Smart-zhi opened 4 years ago
0
Chemistry cannot be identified---cannot perform kinetic analysis

#68 bioxu closed 3 years ago
7
ipdSummary error "M5"

#67 jgonzalez10 closed 5 years ago
8
KeyError: 'FRAMERATEHZ'

#66 istolarek opened 5 years ago
1
Determine significant coverage and score value in the ipdSummary gff

#65 uceleste opened 5 years ago
1
How to set the cap of RAM used during the ipdSummary process

#64 uceleste opened 5 years ago
0
Is it necessary to sort the alignment bam file to run the ipdSummary correctly?

#63 uceleste closed 5 years ago
2
this was accidental post

#62 mille936 closed 5 years ago
0
summarizeModifications Input Question

#61 JohnUrban opened 5 years ago
0
Addition to issues45 and issues46

#60 AlexWanghaoming opened 5 years ago
10
Detecting something different from 4mC, 5mC and 6mA

#59 weedcentipede closed 4 years ago
4
BAM issue

#58 weedcentipede closed 6 years ago
10
IPDsummary with multiple chemistries

#57 clarepacini closed 2 years ago
2
ipdSummary - KeyError: 'DS'

#56 jgonzalez10 opened 6 years ago
14
Does the default value (-1) of "--maxCoverage" mean ALL or ALL - 1. (@4b2bb33)

#55 lemene opened 6 years ago
0
Calculating Methylated Fraction

#54 clarepacini closed 6 years ago
2
IPD mean values

#53 clarepacini opened 6 years ago
3
Found frac=0.000 in output of ipdSummary.py

#52 noirot opened 6 years ago
1