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LieberInstitute
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RNAseq-pipeline
Original version of the RNA-seq pipeline implemented in SPEAQeasy at https://github.com/LieberInstitute/SPEAQeasy.
http://research.libd.org/SPEAQeasy/
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step6 (tx quantification) doesnt run by default with rn6 reference
#62
andrewejaffe
opened
5 years ago
0
Portable RNA-seq pipeline ready for deployment on JHPCE
#61
lcolladotor
opened
6 years ago
0
ERCC step crashes for single end reads
#60
andrewejaffe
opened
6 years ago
0
Integrate with Wrike
#59
lcolladotor
closed
6 years ago
1
11.28.2017
#58
lcolladotor
closed
6 years ago
0
Provide Winter with detailed explanation of LIBD code and example output files
#57
lcolladotor
closed
6 years ago
0
LIBD-Winter Genomics review meeting
#56
lcolladotor
closed
6 years ago
0
12.12.2017
#55
lcolladotor
closed
6 years ago
0
12.19.2017
#54
lcolladotor
closed
6 years ago
0
01.09.2018
#53
lcolladotor
closed
6 years ago
0
look into adding `MISO` as an additional step
#52
andrewejaffe
opened
7 years ago
0
README Example samples.manifest directory does not exist
#51
sportyweiss
closed
7 years ago
1
maybe explore switching to `tximport` for Salmon stuff?
#50
andrewejaffe
opened
7 years ago
0
Improve how R script parses FastQC output
#49
emilyburke
closed
7 years ago
0
can the setup just check if R packages are already installed?
#48
andrewejaffe
closed
7 years ago
0
any memory updates on Salmon?
#47
andrewejaffe
closed
7 years ago
3
add `txNumReads` to the raw counts objects in step7
#46
andrewejaffe
closed
7 years ago
0
add filtering to junctions in counting script
#45
andrewejaffe
closed
7 years ago
0
coverage issues for mouse
#44
andrewejaffe
opened
7 years ago
2
hypthens in the sample names
#43
andrewejaffe
closed
7 years ago
2
update memory requirements
#42
andrewejaffe
closed
7 years ago
0
consider dropping memory needs for variant calling
#41
andrewejaffe
closed
7 years ago
0
typo in step8
#40
andrewejaffe
closed
7 years ago
0
bug in the mouse code, step7, R counts
#39
andrewejaffe
closed
7 years ago
1
Add step to flag swapped samples using called variants.
#38
badoi
closed
7 years ago
0
Document how to create the files in the Annotation folder
#37
lcolladotor
closed
7 years ago
1
make reading in salmon quantification multicore
#36
andrewejaffe
closed
7 years ago
0
Trimming fails
#35
andrewejaffe
closed
7 years ago
5
add option for genotyping samples
#34
andrewejaffe
closed
7 years ago
2
add single + stranded
#33
andrewejaffe
closed
7 years ago
1
add paired + unstranded option
#32
andrewejaffe
closed
7 years ago
1
Trimming check doesn't occur
#31
andrewejaffe
closed
7 years ago
0
Add step for building an RSE from a set of regions
#30
lcolladotor
closed
7 years ago
1
Add step for finding ERs
#29
lcolladotor
closed
7 years ago
0
Create RSE objects
#28
lcolladotor
closed
7 years ago
0
error due to "jaffelab" is missing
#27
cvalenci
closed
7 years ago
3
Error in creating the BigWig files when the data is unstranded
#26
lcolladotor
closed
7 years ago
2
add SRA direct download
#25
andrewejaffe
closed
7 years ago
2
Record job info on logs
#24
lcolladotor
closed
7 years ago
0
shared queue
#23
emilyburke
closed
7 years ago
0
Check that variables in the metrics data frame are of the correct type
#22
lcolladotor
closed
7 years ago
0
Allow specifying sample names
#21
lcolladotor
closed
7 years ago
0
some inconsistency in `jMap`
#20
andrewejaffe
opened
7 years ago
4
incorporate fields from Gencode GTF
#19
andrewejaffe
closed
7 years ago
0
check HISAT2 1 versus 2 pass in current runs
#18
andrewejaffe
closed
7 years ago
1
add step to assess other RNA quality measures
#17
andrewejaffe
opened
7 years ago
4
More flexible and robust option specification
#16
lcolladotor
closed
7 years ago
3
Add a CORES option
#15
lcolladotor
closed
7 years ago
2
delete BAM files if sorted BAM files are created
#14
andrewejaffe
closed
7 years ago
2
add step for quantifying coding SNPs from BAMs
#13
andrewejaffe
closed
7 years ago
3
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