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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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mincov and pad
#108
MikeAxtell
closed
1 year ago
2
ShortStack4 - disable progress bars when non-TTY output
#107
MikeAxtell
closed
1 year ago
2
csfasta support
#106
vojtace
closed
1 year ago
1
Different libraries size
#105
RubioB
closed
1 year ago
1
Annotation of sRNA loci
#104
midhatubaid
closed
1 year ago
1
some question about --pad
#103
dadadawei
closed
1 year ago
0
Problems with shortstack output interpretations
#102
RubioB
closed
1 year ago
2
Does the "--nohp" option return siRNAs only?
#101
uceleste
closed
3 years ago
1
Strandness of PhasiRNAs
#100
Stefano192
closed
1 year ago
4
--pad 0 doesn't work, solution add exists()
#99
ceiabreu
closed
3 years ago
1
Bug: some reads are not placed in clusters properly according to pad/mincov
#98
ceiabreu
closed
1 year ago
2
only one read mapped
#97
DiegoZavallo
closed
1 year ago
1
small RNA annotation using --locifile file
#96
atvivek
closed
3 years ago
2
Characteristics of siRNA clusters
#95
RubioB
closed
3 years ago
1
How to obtain miRNAs name?
#94
Antonio-Nappi
closed
3 years ago
0
Which version of the ShortStack is selected to predict miRNAs in long hairpin structure
#93
Rease123
closed
3 years ago
1
Degraded mRNA
#92
signor-molevol
closed
1 year ago
1
Double tab in Counts.txt
#91
juancresc
closed
1 year ago
3
ranmax 1: avoid choosing primary alignment randomly at all
#90
bbermudez
closed
1 year ago
2
ShortStack padding bug?
#89
bbermudez
closed
1 year ago
3
samtools index: failed to create index
#88
juancresc
closed
5 years ago
4
differential gene expression
#87
mustafaraza1987
closed
3 years ago
1
Multiple bam files input
#86
KaushikPanda1
closed
5 years ago
1
Inaccurate description of Counts.txt in the README
#85
MikeAxtell
closed
1 year ago
1
Separating the known miRNAs from the new clusters identified in ShortStack
#84
tarakaramji
closed
1 year ago
4
How the counts of a small RNA are calculated
#83
arazit
closed
3 years ago
1
Trouble with SOLiD reads
#82
BioFalcon
closed
3 years ago
2
Freezes\out of memory on unplaced small RNAs stage
#81
Chupalav
closed
3 years ago
5
How should we adjust the parameters according to the 2018 Criteria suggested in PlantCell
#80
boya888
closed
1 year ago
1
Target prediction with siRNA clusters
#79
jana33
closed
3 years ago
1
How can I find the "invert_it.pl" wrpper script?
#78
Ashar14
closed
3 years ago
3
why ShortStack is not recognizng input raw read file?
#77
Ashar14
closed
3 years ago
3
Increase multi-mapping positions
#76
DiegoZavallo
closed
3 years ago
3
[question] how to get miRNA sequences for target prediction
#75
juancresc
closed
6 years ago
4
Allow bowtie2 .bam file as --readfile option without realignment
#74
zajakin
closed
1 year ago
1
Corrected bowtie options
#73
zajakin
closed
1 year ago
1
microRNA clusters
#72
BioFalcon
closed
6 years ago
3
Software to draw the dot-bracket RNA secondary structure
#71
sebel76
closed
6 years ago
1
Cluster analysis using ShortStack
#70
arazit
closed
6 years ago
4
Does version 3.8.4 really filter counts by RPM0.5?
#69
Lonelyfighter
closed
6 years ago
6
phasing-phasiRNA prediction
#68
Maja-nib
closed
6 years ago
4
Failed to make fai
#67
juancresc
closed
3 years ago
21
Conda package for ShortStack
#66
sebastian-luna-valero
closed
6 years ago
2
Why some miRNAs members are lacking when MIRNA search is set?
#65
DiegoZavallo
closed
6 years ago
3
Number of mapped reads incorrect
#64
rmonti
closed
6 years ago
6
Which parameters should I use for filtering raw data?
#63
DiegoZavallo
closed
6 years ago
1
Locating bowtie indexes
#62
c-guzman
closed
6 years ago
6
Increasing --pad results in more loci found
#61
groverj3
closed
7 years ago
3
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
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