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brentp
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bwa-meth
fast and accurate alignment of BS-Seq reads using bwa-mem and a 3-letter genome
https://arxiv.org/abs/1401.1129
MIT License
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bwameth set_as_failed=args.set_as_failed
#44
jrmerritt6
opened
6 years ago
6
SNP Question
#43
tantrev
closed
7 years ago
5
bwa-meth and samtools flagstat
#42
anusurendra
opened
7 years ago
8
samtools not found
#41
anusurendra
closed
7 years ago
21
ERNE-BS5
#40
lmanchon
closed
7 years ago
1
WARNING: 5355 reads with length < 80: this program is designed for long reads.
#39
HelloYiHan
closed
7 years ago
2
script to obtain wig or bedgraph for methylation level
#38
Shicheng-Guo
closed
7 years ago
1
Function to remove non-converted non-CpG reads
#37
Shicheng-Guo
closed
1 year ago
1
README update, confused about output
#36
evanbiederstedt
closed
7 years ago
4
--prefix spec in docs breaks bwameth due to new opts pass through functionality
#35
swingingsimian
closed
6 years ago
1
Add a --version option
#34
dpryan79
closed
7 years ago
1
Push out a new release?
#33
dpryan79
closed
7 years ago
2
IOError: Paired End Reads
#32
NicolaLady
closed
1 year ago
8
Added functionality to pass through unkown command line arguments to …
#31
swingingsimian
closed
7 years ago
1
mismatch filter
#30
jklughammer
opened
7 years ago
8
fix unmapped read reporting
#29
jklughammer
closed
7 years ago
0
unmapped reads in c2t converted
#28
jklughammer
closed
7 years ago
2
paired reads not recoqnized as such
#27
cb4github
closed
7 years ago
21
tabulate uses RGSM, but doesn't escape "/"
#26
JohnLonginotto
closed
6 years ago
1
could not make reference genome
#25
aheravi
closed
8 years ago
10
samtools goes awol
#24
JohnLonginotto
closed
6 years ago
3
bed file
#23
Fabunanr
closed
8 years ago
2
Samtools 1.3 support #21
#22
iromeo
closed
8 years ago
1
Samtools 1.3 support
#21
iromeo
closed
8 years ago
2
adding passing options to bwa mem
#20
avilella
closed
5 years ago
3
aligning to CTOT+CTOB -- equivalent of bismark --pbat
#19
avilella
opened
8 years ago
5
[fputs] Broken pipe
#18
acgtun
closed
8 years ago
9
running bwameth.py tabulate on Ecoli data
#17
avilella
closed
6 years ago
1
Added a --nome option to tabulate to support NOMe-seq data ie to call CpG vs GpC methylation
#16
astatham
closed
9 years ago
1
Broken pipe, no alignments written to bam file.
#15
markussa
closed
9 years ago
3
'samtools sort' memory limit
#14
superbobry
closed
9 years ago
2
implement Yaping's suggestions for WGBS Bis-SNP
#13
ttriche
closed
9 years ago
1
Broken pipe at samtools index
#12
will-NYGC
closed
9 years ago
5
Faster 'convert_fasta' and 'as_bam'
#11
superbobry
closed
6 years ago
5
Better modularity
#10
superbobry
closed
6 years ago
4
Disallow RC alignments
#9
superbobry
closed
10 years ago
1
Installation problem
#8
ikron
closed
10 years ago
2
'samtools' errors aren't reported in 'as_bam'
#7
superbobry
closed
9 years ago
0
UnboundLocalError: local variable 'toks' referenced before assignment
#6
superbobry
closed
10 years ago
16
Multiple sets of FASTQ files
#5
superbobry
closed
10 years ago
4
Relax Python version restrictions
#4
superbobry
closed
10 years ago
2
Test fail: both release 0.9 and git cloned
#3
vogelwk
closed
9 years ago
21
Missing kmer when using GSNAP in compare/README?
#2
PeteHaitch
closed
10 years ago
0
Error in tabulation of example
#1
jvhaarst
closed
10 years ago
4
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