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nanoporetech
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megalodon
Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
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megalodon.megalodon_helper.MegaError: Data covering index does not exist.
#257
Fatihlrcfs
opened
2 years ago
3
Bam with IGV has different results from modified_bases.5mc.bed
#256
muguading
closed
2 years ago
1
running megalodon and then the system breakdown
#255
BaylorLyu
closed
2 years ago
0
GPU works abnormal in guppy=6.0.1 & megalodon=2.4.1
#254
BaylorLyu
closed
2 years ago
4
python3.9 update README
#253
jowodo
closed
2 years ago
1
Expected release of all-context methylation models for kit 12?
#252
Kirk3gaard
opened
2 years ago
2
How to use estimate_threshold to modify --mod-binary-threshold
#251
jeffsteimle
closed
2 years ago
4
Custom Remora models
#250
CodingKaiser
closed
2 years ago
1
Why do some reference CGs not have Mm/Ml entries in mod_mappings.bam?
#249
benbfly
closed
2 years ago
14
What's default way to call 5mC only in Remora?
#248
liuyang2006
closed
2 years ago
1
modified_bases.5mC.bed gets very different results than running modbam2bed on mod_mappings.bam
#247
benbfly
closed
2 years ago
35
Instruction about mod_mapping format
#246
vahidAK
opened
2 years ago
5
Megalodon/rerio issue
#245
0Bernhard
closed
2 years ago
6
ERROR: Modified bases database already exists. Either provide location for new database or open in read_only mode.
#244
ViHammer
closed
2 years ago
6
Guppy v6.0.1 with megalodon Rerio model running error on GPU
#243
liuyang2006
closed
2 years ago
4
Unlimited CPU use with remora
#242
kpalin
closed
2 years ago
1
segfault in remora/model_util.py load_onnx_model()
#241
benbfly
closed
2 years ago
3
How to run megalodon without guppy?
#240
wangzhennan14
closed
2 years ago
6
Remora parameter question 5hC_5mC vs 5mC
#239
Eric-CH-Chen
opened
2 years ago
2
Guppy 6.0.1 problems ...
#238
benbfly
closed
2 years ago
3
[Question] Does using Megalodon for just mappings make sense?
#237
fidibidi
closed
2 years ago
2
3 most common unsuccessful processing stages
#236
zmz1988
closed
2 years ago
4
[guppy/error] File name too long. Error initialising basecall server using port:
#235
uros-sipetic
closed
2 years ago
4
Best practices training from scratch using only modified inputs
#234
CodingKaiser
closed
2 years ago
1
Question on mappings.bed output formats
#233
wentski
closed
2 years ago
3
guppy_server_initialization
#232
0Bernhard
closed
2 years ago
5
Megalodon Extras: Ref File-Case sensitive
#231
jcolicchio-soundag
opened
2 years ago
0
Could I use config file for MinION/GridION to deal with fast5 produced by PromethION?
#230
mantonglaw
closed
2 years ago
1
Guppy server initialization failed.
#229
twslocum
closed
2 years ago
6
Megalodon hangs when running on multi-fast5 files.
#228
Subhanjanb
closed
2 years ago
2
Calibrating a from-scratch modified base model
#227
CodingKaiser
closed
2 years ago
1
Megalodon ignores "--use_tcp" from guppy6
#225
billytcl
closed
2 years ago
2
Conda installs megalodon version 2.3.5 instead of 2.4.0.
#224
snamburi3
closed
2 years ago
1
Performing ONLY modified basecalling (terminating before aggregation)
#223
mvolar
closed
2 years ago
3
Proper guppy config file for MinION methylation
#222
cstill3928
closed
2 years ago
1
Interpretation of bedmethyl file
#221
amauryavril
closed
2 years ago
1
megalodon_extras aggregate run, log.aggregation.re_aggregated.txt not found
#220
danrdanny
closed
2 years ago
4
Aggregation does not start
#219
amauryavril
closed
2 years ago
1
PermissionError: [Errno 13] Permission denied: '/home/z/MegalodonTest/ont-guppy/bin/'
#218
CSU-ZeyuZhong
closed
3 years ago
2
Encountered malformated fast5 ::: Unable to get link info (incorrect metadatda checksum after all read attempts)
#217
tpesout
closed
2 years ago
4
Can we take aligned BAM file as input to generate variant calls by megalodon?
#216
emily288
closed
2 years ago
1
Guppy server returned invalid read: 'movement'
#215
danrdanny
closed
3 years ago
1
Error Running megalodon-2.3.5
#214
onkar2470
closed
3 years ago
1
Megalodon analysis freeze because of computing ressources ?
#213
pterzian
closed
2 years ago
3
Understanding megalodon output in IGV
#212
danrdanny
closed
3 years ago
9
Can't install megalodon
#211
juliofinalet
closed
3 years ago
4
Unexpected errors in Megalodon v2.3.5
#210
billytcl
closed
2 years ago
3
struct.error: 'i' format requires -2147483648 <= number <= 2147483647
#209
amauryavril
closed
2 years ago
4
Using miscalled bases for training methylation callers
#208
CodingKaiser
closed
3 years ago
7
ERROR: Guppy server initialization failed. See guppy logs in [--output-directory] for more details.
#207
Fatihlrcfs
closed
3 years ago
1
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