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MikeAxtell
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ShortStack
ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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Reducing redundancy of reads
#60
pgonzale60
closed
6 years ago
2
How to deal with ShortStack Counts.txt files?
#59
DiegoZavallo
closed
7 years ago
6
Trouble with Bowtie
#58
mmageroy
closed
7 years ago
7
Problem with ShortStack 3.8.2
#57
xuhangliu
closed
7 years ago
2
Adjustable cutoff for calling locus 'strand'
#56
MikeAxtell
closed
7 years ago
1
bowtie and bowtie-build required even for runs with no alignment
#55
MikeAxtell
closed
7 years ago
1
Cluster calling on 'stitched' genomes spans stitched segments
#54
MikeAxtell
closed
7 years ago
1
Error with TEST_DATA
#53
dwightkuo
closed
7 years ago
4
.fq.gz input file format issue
#52
pedrocrisp
closed
7 years ago
4
length of MajorRNA does not match dicer call
#51
rmonti
closed
7 years ago
3
expected index names
#50
rmonti
closed
6 years ago
4
--outdir
#49
rmonti
closed
7 years ago
1
Locus coordinates
#48
rmonti
closed
7 years ago
1
Major incompatibility with bowtie 1.2.0
#47
MikeAxtell
closed
7 years ago
1
Discrepancy between MeanReads and Reads
#46
MikeAxtell
closed
7 years ago
2
Readgroup names
#45
rmonti
closed
7 years ago
3
inv_file option
#44
mgalland
closed
7 years ago
2
3.5 Some quality values remain in bam files
#43
MikeAxtell
closed
7 years ago
1
A bug when parsing file names?
#42
naumenko-sa
closed
7 years ago
5
Questions about the software ShortStack. (e-mail to you, too)
#41
Linhua-Sun
closed
7 years ago
3
Adding extra flags to bowtie
#40
adomingues
closed
7 years ago
3
Recongition of file extensions is patchy
#39
adomingues
closed
7 years ago
3
Error running TEST_DATA
#38
d3d1y
closed
7 years ago
6
ShortStack version 3.4 -- O-tagged reads are not always stored in the original orientation
#37
shahsam
closed
7 years ago
1
ChIP-seq
#36
adomingues
closed
7 years ago
4
ShortStack3.3 MIRNA loci description files
#35
alicelunardon
closed
7 years ago
1
incorrect alignments with very large genomes (bowtie issue)
#34
MikeAxtell
closed
8 years ago
1
cutoff for phasescore
#33
xingwu2
closed
8 years ago
2
total counts vary between alignment and sum of observed counts
#32
xingwu2
closed
8 years ago
2
NAs in Counts.txt
#31
xingwu2
closed
8 years ago
2
How to only count the alignments without any other analyses in the newest Shortstack
#30
xingwu2
closed
8 years ago
1
Is Shortstack sensitive to detect small RNAs that do not exist in reference genome
#29
xingwu2
closed
8 years ago
1
Too many MIRNA duplex
#28
xingwu2
closed
8 years ago
6
Out of memory message
#27
MikeAxtell
closed
8 years ago
3
Option request .. change limit of RNAfold size during MIRNA finding
#26
MikeAxtell
closed
8 years ago
1
RNA folding always fails at step7
#25
RafaelMViana
closed
8 years ago
19
Experiment with increasing memory to samtools sort
#24
MikeAxtell
closed
9 years ago
1
Improve gff3 files
#23
MikeAxtell
closed
9 years ago
2
warning in STDERR about non-numeric argument in de-novo cluster identification/analysis phase
#22
shahsam
closed
9 years ago
6
Add multi-threading for samtools view and sort operations
#21
MikeAxtell
closed
9 years ago
1
[bam_header_read] EOF marker is absent. The input is probably truncated.
#20
MikeAxtell
closed
9 years ago
1
Colons in chromosome names cause disaster
#19
MikeAxtell
closed
9 years ago
1
Can you add some demo files?
#18
wangqinhu
closed
9 years ago
8
recursive counting of read groups fails
#17
MikeAxtell
closed
9 years ago
1
Failure to count loci after encountering a chr. with zero reads
#16
MikeAxtell
closed
9 years ago
1
calling MIRNAs with count mode
#15
MikeAxtell
closed
9 years ago
1
maple slow on some clusters ... data look-up speed matters
#14
MikeAxtell
closed
9 years ago
2
super slow in miRNA finding if genome is fragmented
#13
MikeAxtell
closed
9 years ago
1
Support needed for ebwtl extension made by bowtie 1.1.1
#12
MikeAxtell
closed
9 years ago
1
Capture log information from butter, maple, bam2wig in the master ShortStack output
#11
MikeAxtell
closed
9 years ago
1
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