liyu95 DeepSimulator issues

liyu95 / DeepSimulator

The first deep learning based Nanopore simulator which can simulate the process of Nanopore sequencing.

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issues

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Where is DTW performed during training? What is the Signal_To_Event binary doing? Still maintained?

#58 maximilianmordig opened 11 months ago
0
-nan of 0 (pass 0 + fail 0) reads passed base-calling

#57 liushuqing506 opened 1 year ago
0
Questions about the usage of this tool

#56 HLHsieh opened 1 year ago
0
Events at the output Fast5

#55 parsboy66 opened 1 year ago
0
length of the reads

#54 parsboy66 opened 1 year ago
0
Is this model still being developed?

#53 raadmahmoudkromek opened 1 year ago
0
double number of reads given by -n read_num

#52 Psy-Fer opened 2 years ago
0
Issue with small reference contigs

#51 Csam488 opened 2 years ago
0
Related to tuning of Repeat time

#50 subhasiny opened 3 years ago
5
Signal generator 1.5 trained using R9 or R10 flowcell chemistry?

#49 Linkrw12 opened 3 years ago
3
mapping from alignment paf file or pass/fail.fastq to the sampled_read_processed_genome_*.fasta

#48 YantingHuang opened 3 years ago
1
replicate read id

#47 N-damo closed 3 years ago
0
Correct type in arg parser help string

#46 fanzhuyifan closed 3 years ago
0
Support for simulating more recent base-callers Guppy 3.6

#45 cjain7 opened 4 years ago
2
Error in pore_model.sh

#44 Jenny-dan opened 4 years ago
1
TensorFlow

#43 solomonchak opened 4 years ago
2
Issue about same repeated simulates

#42 renzilin closed 4 years ago
1
Bug in checking accuracy

#41 renzilin closed 4 years ago
3
dRNA with or without modifications?

#40 pabloacera opened 4 years ago
1
multi fasta input

#39 alstonius opened 4 years ago
2
Please include a notice to not have a conda env active during install

#38 patbohn opened 4 years ago
0
Install on MacOs

#37 arsthilaire closed 4 years ago
1
Use a readlinkf.sh implementation in the repo instead of native readlink

#36 ExplodingCabbage closed 4 years ago
1
update the replace n function

#35 liyu95 closed 4 years ago
0
Discontinuous fasta

#34 liyu95 closed 4 years ago
0
Pre-process input error with a multiple chromosome file like 'GRCh38.p12.genome.fa'

#33 zhixue closed 4 years ago
10
Amplicon reads simulation

#32 MaestSi closed 4 years ago
3
DeepSimulator (branch discontinuous-fasta) dosen't handle multi-line fasta files correctly

#31 yjx1217 closed 4 years ago
5
Simulation from multiple contigs in Multi-FASTA

#30 JakubBartoszewicz closed 5 years ago
5
A potential bug related with read coverage for v1.5?

#29 yjx1217 closed 5 years ago
2
libcuda.so.1 problem when run deep_simulator.sh

#28 Lemon-Liu closed 5 years ago
1
some questions about the model graph code

#27 huangnengCSU opened 5 years ago
0
Switch to conda activate/deactivate

#26 zdk123 closed 5 years ago
1
Short strands sequencing

#25 evgisa closed 5 years ago
2
[suggestion] update for latest conda/python

#24 zdk123 opened 5 years ago
7
Experiment

#23 liyu95 closed 5 years ago
0
read length

#22 rberrens closed 5 years ago
2
new error model

#21 yjx1217 closed 5 years ago
12
guppy

#20 lfaino closed 5 years ago
2
About Low pass filter and tuning sample

#19 AriBad closed 5 years ago
8
steps for training

#18 brianwalenz opened 5 years ago
2
Typo in installation

#17 telatin closed 5 years ago
0
Under-sampling both ends of reference genome

#16 evgisa closed 5 years ago
3
DeepSimulator may overide specified thread numbers (-c )

#15 yjx1217 closed 5 years ago
1
[feature suggestion] adding an option to control random seed?

#14 yjx1217 closed 5 years ago
2
[feature suggestion] adding an option to specify desired read coverage?

#13 yjx1217 closed 5 years ago
3
-M simulator parameter

#12 evgisa closed 5 years ago
2
Default length distribution

#11 evgisa closed 5 years ago
3
Unable to run the install script

#10 samyuktr closed 5 years ago
1
RNA-seq simulation

#9 daniellezhang closed 5 years ago
2