issues
search
dieterich-lab
/
DCC
DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates.
https://dieterichlab.org/software/
GNU General Public License v3.0
36
stars
20
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated
#57
giuseppe0525
closed
5 years ago
2
DCC installation error
#56
giuseppe0525
closed
5 years ago
2
Question about RNA prep kit supported by DCC
#55
giuseppe0525
closed
5 years ago
2
the "circRNA read counts" in output file
#54
circR
closed
5 years ago
2
Fail at 'Filter by non repetitive region'
#53
bioysu
opened
5 years ago
3
stop at Using files _tmp_DCC/tmp_circCount and _tmp_DCC/tmp_coordinates for filtering
#52
ChrisLou-bioinfo
closed
2 years ago
4
Problem during host gene expression counting
#51
BaluPai
closed
6 years ago
6
Strand information is now included in CircSkipJunctions file
#50
tjakobi
closed
6 years ago
0
Fix issue 47
#49
tjakobi
closed
6 years ago
0
CircSkipJunctions does not contain junction orientation
#48
CDieterich
closed
6 years ago
3
Dubious CircSkipJunctions output
#47
CDieterich
closed
6 years ago
3
gene name annotations not included in final results
#46
fklirono
closed
6 years ago
3
Cannot provide mate separate mapping BAMs to -B list
#45
plmsuper8
closed
6 years ago
4
DCC errors out looking for bam index/sorted bam
#44
ShobanaSekar
closed
6 years ago
6
guessing one bam or all inputs
#43
jorgeboucas
opened
6 years ago
0
DCC crashes with -fg set and -M unset
#42
tjakobi
closed
6 years ago
11
groupBy won't group
#41
bchen4
closed
6 years ago
2
extract the circRNA sequences using the script getcircfasta
#40
tigerxu
closed
7 years ago
3
Single End Read run crashes
#39
CDieterich
closed
7 years ago
0
Check for sorted BAM files fails if first chromosome has less than 100 mapped reads
#38
tjakobi
closed
7 years ago
0
two different junction type for the same circ?
#37
alexey0308
opened
7 years ago
4
BAM error
#36
tjakobi
closed
5 years ago
9
Normalization of expression of circRNA
#35
xflicsu
closed
3 years ago
2
gene feature annotation looks incorrect
#34
CDieterich
opened
7 years ago
0
cant find 'tmp_unsortedNoChrM'
#33
FranziMe
closed
7 years ago
2
Check correctness of stranded work flow
#32
tjakobi
opened
7 years ago
4
IndexError: list index out of range
#31
cmonger
closed
7 years ago
11
fails if -R is not set
#30
alexey0308
closed
7 years ago
0
temporary file problem
#29
CDieterich
closed
7 years ago
2
Temporary file names for circRNA counts are wrongly concatenated
#28
tjakobi
closed
7 years ago
0
DCC output directory needs to be created before logging starts
#27
tjakobi
closed
7 years ago
0
CircCoordinate file gene annotation conatins only "." when run without -ss
#26
tjakobi
closed
7 years ago
2
DCC does not check if annotation file is present during start
#25
tjakobi
closed
7 years ago
0
Linear count files only contain zero values and no actual counts
#24
tjakobi
closed
7 years ago
0
SJ.out.tab and BAM file requirements are not part of the documentation
#23
tjakobi
closed
7 years ago
0
-temp / -k option: file cleanup does not work and fails for some files
#22
tjakobi
closed
7 years ago
1
Check functions of the CircSkip routines
#21
tjakobi
closed
7 years ago
1
convertjunctionfile2bamfile() fails if BAM files are not named in STAR fashion
#20
tjakobi
closed
8 years ago
0
Check if input BAM files are sorted by coordinate
#19
tjakobi
closed
7 years ago
0
Find reason for very slow circRNA detection phase
#18
tjakobi
opened
8 years ago
0
Allow user to specify temporary location of DCC generated files
#17
tjakobi
closed
8 years ago
0
Allow user to specify output location of DCC generated files
#16
tjakobi
closed
8 years ago
0
Replace console logging via "print" with a proper logging facility
#15
tjakobi
opened
8 years ago
0
DCC log file does not report the command line anymore
#14
tjakobi
closed
8 years ago
0
Deletion of CircSkip temp files crashes if no CircSkip files present
#13
tjakobi
closed
8 years ago
0
Annotation in develop branch produces different results
#12
tjakobi
closed
8 years ago
0
Problem with temporary file handling during mpileup
#11
tjakobi
closed
8 years ago
1
CircCoordinates has not column labels anymore
#10
CDieterich
closed
8 years ago
2
Single end reads and function checkjunctionfiles
#9
CDieterich
closed
8 years ago
3
Problem with empty Chimeric junction files
#8
CDieterich
closed
8 years ago
0
Previous
Next