zstephens neat-genreads issues

zstephens / neat-genreads

NEAT read simulation tools

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issues

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golden BAM?

#106 xmy1990 opened 3 months ago
1
IndexError: list index out of range

#105 mariaelf97 opened 7 months ago
1
update deprecated biopython functions

#104 tturowski closed 1 year ago
1
SequenceContainer.py fails with missing attribute in Seq object

#103 Npaffen opened 1 year ago
4
Bump numpy from 1.19.5 to 1.22.0

#102 dependabot[bot] opened 2 years ago
0
Expression levels

#101 ninaxiong11 opened 2 years ago
1
Bed file with more regions than reference

#100 MikeWLloyd closed 2 years ago
1
Potential bug in compute_fraglen.py

#99 mrmilhaven opened 3 years ago
2
Identical forward and reverse sequences for half of the reads in FASTQ files

#98 Accio closed 3 years ago
1
Plot failed

#97 yangyxt opened 3 years ago
0
optimize logging, only stderr is real-time logging

#96 yangyxt opened 3 years ago
0
Bug fix and couple minor improvements

#95 tprodanov opened 3 years ago
1
Prolonged Execution - any tips on how to parallelise execution on v3.0

#94 warjaSBG closed 3 years ago
1
Simulating genomes with complex ploidy

#93 Militeee opened 3 years ago
1
gen_reads.py produces empty output files

#92 joys8998 closed 3 years ago
2
Bam input into compute_fraglen.py measures read length rather than insert size

#91 jeffpbruce closed 3 years ago
1
Minor notation change

#90 joshfactorial closed 3 years ago
0
Genreads overhaul

#89 joshfactorial closed 3 years ago
0
Genreads overhaul

#88 joshfactorial closed 3 years ago
1
Simulate SNPs only without indels

#87 aaronkwc closed 3 years ago
1
GRCH38 problems

#86 popicka opened 4 years ago
3
Genreads overhaul

#85 joshfactorial closed 4 years ago
0
Null Sequencing Error Model

#84 cilliannolan closed 4 years ago
2
"Something went wrong with the generated fasta file" error message with bacterial genreads wrapper

#83 bhanugandham opened 4 years ago
4
Standard deviation of coverage

#82 multimeric closed 3 years ago
1
Multiple records with the same position in the golden VCF file

#81 mohammedkhalfan opened 4 years ago
1
error with read length

#80 alxsm opened 4 years ago
3
Sequencing error rate question for whole genomes.

#79 anushishah opened 4 years ago
0
Sequencing error rate for long reads not as specified

#78 reinator closed 4 years ago
2
Dealing with generic bases (N's) in the reference genome

#77 reinator closed 4 years ago
1
Create tumor/normal pairs with CNVs

#76 popicka opened 4 years ago
3
error when running genReads.py

#75 michalsharabi closed 4 years ago
3
Python3 conversion

#74 meridith-e closed 4 years ago
0
Python3 conversion

#73 meridith-e closed 4 years ago
0
Add note about pysam not working on windows

#72 meridith-e closed 4 years ago
0
trouble with computeGC.py

#71 RichardCorbett opened 4 years ago
4
question about coverage

#70 kkamii opened 4 years ago
1
question about sequencing error rate

#69 kkamii closed 4 years ago
2
VCF problem: IndexError: string index out of range_

#68 gonzalpk closed 4 years ago
5
Question about coverage

#67 kkamii closed 4 years ago
2
ValueError: invalid literal for int() with base 10: '1.0086e+06'

#66 schmeing closed 5 years ago
1
IndexError: list index out of range

#65 schmeing closed 5 years ago
8
parameter '-to' not working as expected

#64 mrpk123 opened 5 years ago
2
Simulation of fixed read numbers (incl. low coverage)

#63 tloka closed 5 years ago
2
No output in Golden VCF

#62 senzhaocode closed 5 years ago
3
Getting memory error while using hg19 as reference and targeted bed file for whole exome

#61 mrpk123 opened 5 years ago
4
Question about mutation models

#60 XavierMialhe opened 5 years ago
1
CIGAR related error in read simulations

#59 ju-mu closed 5 years ago
8
Error in read simulation after patch for issue #56

#58 ju-mu closed 5 years ago
1
Insert SVs in vcfs

#57 jackieduckie opened 5 years ago
2