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caleblareau
/
mgatk
mgatk: mitochondrial genome analysis toolkit
http://caleblareau.github.io/mgatk
MIT License
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Process 10x-scRNA-seq data using mgatk
#44
pxh251
closed
2 years ago
19
BioRad scATAC-seq data
#43
liaojinyue
closed
2 years ago
1
Cell count difference in the mgatk outputs and scATAC-seq cell ranger outputs
#42
Chhiring-Lama
closed
2 years ago
1
can be used for snATAC?
#41
AnjaliC4
closed
2 years ago
1
Using call mode for bulk RNA-seq data.
#40
francat
closed
2 years ago
1
initial commit
#39
bobermayer
closed
3 years ago
1
Error with bcall mode
#38
Arkosen
closed
2 years ago
7
Assume sorted bam
#37
cnk113
closed
2 years ago
3
How to limit the virtual memory use of mgatk
#36
jimlin1668478052
closed
2 years ago
2
Missing input files for rule call_variants
#35
FloWuenne
closed
2 years ago
10
Clarification on marking duplicates
#34
cnk113
closed
3 years ago
7
Handle overlap and variant calling
#33
vincent6liu
closed
3 years ago
1
mgatk does not generate .rds output files
#32
mjprzybilla
closed
3 years ago
2
Error in .local(assays, ...) : unused argument (rowData = <S4 object of class "GRanges">)
#31
francat
closed
3 years ago
3
Failed to open file "CRA_test1_mgatk/temp/temp_bam/barcodes.8.temp0.bam" : No such file or directory
#30
bio-ruxandra-tesloianu
closed
2 years ago
22
chunk_barcoded_bam.py issue
#29
JohnApp-scRNA
closed
3 years ago
6
Fix umi_barcode value in <name>.parameters.txt output file
#28
AustinHartman
closed
3 years ago
2
mgatk consensus read formation
#27
JohnApp-scRNA
closed
3 years ago
2
Filtering variants
#26
PasLukas
closed
3 years ago
5
Using scRNA
#25
PasLukas
closed
3 years ago
1
Environment setup
#24
JohnApp-scRNA
closed
3 years ago
4
Use mitochondria genome only or use all chromosomes
#23
Puriney
closed
3 years ago
2
Error in rule make_depth_table: 'InputFiles' object has no attribute 'depths'
#22
heruiyang
closed
3 years ago
6
Missing files due to improper folder specification
#21
mathosi
closed
4 years ago
18
del viz
#20
caleblareau
closed
4 years ago
2
discard base quality by default but keep it with flag
#19
caleblareau
closed
4 years ago
1
wiki
#18
caleblareau
closed
4 years ago
0
click echo bam file being analyzed
#17
caleblareau
closed
5 years ago
1
Force upper case in reference
#16
caleblareau
closed
5 years ago
1
`bcount` mode
#15
caleblareau
closed
5 years ago
1
snake make log / stats
#14
caleblareau
closed
5 years ago
1
UMIs for 3' / 5' sequencing data
#13
caleblareau
closed
5 years ago
1
split R package and python package
#12
caleblareau
closed
5 years ago
0
Max cell IDs
#11
caleblareau
closed
5 years ago
1
read tag
#10
caleblareau
closed
6 years ago
1
check .snakemake directory
#9
caleblareau
closed
6 years ago
0
empty bam file
#8
caleblareau
closed
5 years ago
1
samtools external dependency / fastq mean BAQ
#7
caleblareau
closed
6 years ago
1
Watson/crick stand
#6
caleblareau
closed
6 years ago
1
cluster scatter
#5
caleblareau
closed
6 years ago
0
MultiAssayExperiment
#4
caleblareau
closed
6 years ago
0
cambridge mitochondrial genome
#3
caleblareau
closed
6 years ago
2
circular mitochondrial genome
#2
caleblareau
closed
6 years ago
2
AF > 1
#1
caleblareau
closed
6 years ago
1
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