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nunofonseca
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irap
integrated RNA-seq Analysis Pipeline
GNU General Public License v3.0
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Fixed mem levels
#58
pinin4fjords
closed
6 years ago
1
Fixed check for local download folder, fixed sed pattern (needed literal escaped '.'s)
#57
pinin4fjords
closed
6 years ago
0
Sed needs full stops to be escaped to achieve desired meaning
#56
pinin4fjords
closed
6 years ago
0
TPM values rounded to 2 decimals
#55
freekvh
closed
6 years ago
3
RSEM strandness
#54
ghost
closed
6 years ago
12
failed to load GTF file
#53
byb121
closed
5 years ago
3
our_prefix error when analysis name is same as the raw read file name without suffix
#52
byb121
closed
5 years ago
2
BiomaRt is a dependency of Scater, install it first
#51
pinin4fjords
closed
6 years ago
1
irap_raw2metric no html file, not gzipped
#50
freekvh
closed
5 years ago
7
mapper options in config file is ignored
#49
byb121
closed
6 years ago
3
Not handling 'qual_filtering=none' as expected
#48
byb121
closed
6 years ago
1
contamination genomes built with bowtie2 won't be recognised in contamination filtering
#47
byb121
closed
6 years ago
1
compress FastQ?
#46
byb121
closed
6 years ago
1
bamToFastq produces overwhelming warnings due to secondary alignments
#45
byb121
closed
6 years ago
1
Feature/ubuntu dockstore
#44
byb121
closed
6 years ago
1
file existence check
#43
byb121
closed
6 years ago
1
-R is ignored when R is not preinstalled
#42
byb121
closed
6 years ago
1
bamToFastq pickup the wrong bam file name
#41
byb121
closed
6 years ago
2
No rule to make target
#40
jodyphelan
closed
6 years ago
3
Quantify the amount of rRNA in a library/sequencing experiment
#39
freekvh
closed
6 years ago
3
Contamination check errors
#38
freekvh
closed
6 years ago
4
how to norm the multiple bio replication TPM values into one tissue/condition value?
#37
wangyugui
closed
6 years ago
2
Merging Matrices in libTSVAggrTransByGene fails?
#36
Niklas123Niklas
closed
6 years ago
20
more guideline for Atlas SOP
#35
wangyugui
closed
6 years ago
2
Why the "samtools view -F 4" and the split of tsv files
#34
freekvh
closed
6 years ago
2
Problem with Report generation
#33
Niklas123Niklas
closed
6 years ago
10
missing file on R component
#32
PeteClapham
closed
5 years ago
5
Add to Dockstore with CLW mapping
#31
keiranmraine
opened
7 years ago
1
Could pre-compiled binaries by considered as part of an installation method ?
#30
PeteClapham
closed
7 years ago
4
Strandedness setting in iRAP conf
#29
freekvh
closed
7 years ago
2
make: *** No rule to make target '
#28
jodyphelan
closed
7 years ago
11
gnpplot
#27
jodyphelan
closed
6 years ago
3
Unknown regexp modifier "/t" at (eval 1) line 1, at end of line
#26
jodyphelan
closed
7 years ago
4
Set to 85% of the read by default
#25
freekvh
closed
6 years ago
13
Bug?
#24
Niklas123Niklas
closed
7 years ago
8
IGV_VERSION=2.1.24
#23
freekvh
closed
7 years ago
3
Problem dry-running the ecoli_ex.conf file
#22
ikramu
closed
7 years ago
2
VM errors
#21
freekvh
closed
7 years ago
4
No multithread for bowtie2-build
#20
Niklas123Niklas
closed
7 years ago
12
Error running irap_install.sh
#19
Niklas123Niklas
closed
7 years ago
5
normalization of counts returns an error
#18
stkachev
closed
7 years ago
4
Latest docker image is not tagged
#17
moskalenko
closed
8 years ago
1
Update instructions
#16
dsarov
closed
8 years ago
1
Error at piano step of irap
#15
syedarshi
closed
9 years ago
1
Solves wrong order of data columns provided to DESeq2
#14
pcm32
closed
9 years ago
0
Password Protected Issue While Extracting/Decompressin iRAP Files
#13
WEESHEANFOO
closed
9 years ago
3
irap install within docker image fails on Perl GD-2.56 module installation
#12
GoogleCodeExporter
closed
9 years ago
1
Error in dockerfile, should use WORKDIR <dir> instead of RUN cd <dir>
#11
GoogleCodeExporter
closed
9 years ago
1
Suggestion
#10
GoogleCodeExporter
closed
9 years ago
2
I am using iRAP to do a differential expression analysis between two groups made by two biological replicates each. Sequencing was performed with 454, so reads are on average longer than 200nt. I ran iRAP two days ago, but now it seems that the process has been slowed in a step requiring the use of R, but I don't understand which one. I attach to this message the log file generated during the process.
#9
GoogleCodeExporter
closed
9 years ago
3
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