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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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README does not describe the custom tags in BAM files.
#156
MikeAxtell
opened
5 days ago
0
Better reporting of read trimming
#155
MikeAxtell
opened
4 weeks ago
0
how to reserve the U&P reads of alignment bam file?
#154
Yuzhang0102
opened
1 month ago
1
Start position in FastA description lines off by one from start position in GFF3
#153
kubu4
closed
1 month ago
3
Fast Alignment Mode or disable browser tracks by default
#152
MikeAxtell
closed
2 months ago
1
shortstack4.0.3 ValueError: invalid literal for int() with base 10: ''
#151
joweihsieh
opened
2 months ago
16
Counts.txt file not created when using .bam files as input
#150
mikrzol
closed
1 month ago
8
ShortStack on mRNA data?
#149
meerveld96
closed
2 months ago
2
Inconsistencies Between Default Settings in Documentation and Code
#148
spriego
closed
2 months ago
1
Low mapping rate during Bowtie
#147
SaelinB
closed
2 months ago
1
IndexError: list index out of range during "Screening of possible de novo microRNAs"
#146
kubu4
closed
2 months ago
17
Results
#145
aayoungfish
closed
2 months ago
1
_csv.Error: field larger than field limit (131072)
#144
kaspartom
closed
7 months ago
5
IndexError: list index out of range at very beginning of alignment stage
#143
kubu4
closed
8 months ago
1
--pad 200 issue
#142
KJeynesCupper
closed
7 months ago
2
conda installs 3.8.5 not newer versions
#141
alansill
closed
7 months ago
1
ShortStack version 4.0.2: IndexError: list index out of range
#140
Maja-nib
closed
7 months ago
2
complexity measurement
#139
thalescherubino
closed
7 months ago
1
Problem with de novo miRNA annation with SS 4.0.2
#138
FlaviaPavan
closed
7 months ago
4
Update ShortStack
#137
y9c
opened
11 months ago
1
"IndexError when selecting alignment in al_pass_2 in ShortStack"
#136
zhongxiangSu
closed
11 months ago
5
SS 3.8.5 vs 4.0.1
#135
kattri811
closed
7 months ago
2
Malformed gff3 and incorrect reporting for MIRNA loci when using --locifile
#134
MikeAxtell
closed
1 year ago
1
Criteria for defining MIRNA and other types of sRNA
#133
SergioRodLla
closed
1 year ago
2
Conda installing bowtie-build 1.0.0 by default
#132
thalescherubino
closed
7 months ago
2
Option --locifile and MIRNA locus finding
#131
MikeAxtell
closed
1 year ago
1
IndexError: list index out of range
#130
meerveld96
closed
1 year ago
11
Multiple BAM files or merged BAM file not working
#129
somnya
closed
1 year ago
7
siRNAs identification
#128
ozambadam
closed
1 year ago
1
multiply mapped sRNA in Counts.txt
#127
AlineMuyle
closed
1 year ago
2
Too many predicted sRNA are longer than 300nt
#126
Yuzhang0102
closed
1 year ago
1
cutadapt extra trimming
#125
crisalves80
closed
7 months ago
6
Fixed typos in README.md
#124
GuyTeichman
closed
1 year ago
0
Trying to run ShortStack with the --knownRNAs argument, it does not work
#123
ozambadam
closed
1 year ago
5
ShortStack 4.0.0 does not install in ubuntu 22.04
#122
cche
closed
1 year ago
13
possibility to increase the 50 multi-mapping treshold from bowtie with the last version ?
#121
arnauddr37
closed
1 year ago
2
QIAseq® miRNA Library paired-end reads for sRNA-seq experiment
#120
DiegoZavallo
closed
1 year ago
2
Cannot generate the wigToBigWig file on large genome
#119
sebel76
closed
1 year ago
3
Indexing Bam files for large genome mapping
#118
sebel76
closed
1 year ago
12
No phasiRNA annotation on ShortStack 4.0.0?
#117
sebel76
closed
1 year ago
1
ShortStack 4.0.0 return empty StructVis files
#116
sebel76
closed
1 year ago
5
Check wigToBigWig executable up front
#115
MikeAxtell
closed
1 year ago
2
FASTA format is unsupported for upgrade (4.0)
#114
RJEGR
closed
1 year ago
3
bioconda recipe for release 4.0.0
#113
MikeAxtell
closed
1 year ago
1
ShortStack4
#112
MikeAxtell
closed
1 year ago
0
miRNA calls - restrict to 21, 22 nt mature miRNAs
#111
MikeAxtell
closed
1 year ago
1
miRNA outputs
#110
MikeAxtell
closed
1 year ago
1
ShortStack4 : Formatting of gff3 files
#109
MikeAxtell
closed
1 year ago
1
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
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