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mhammell-laboratory
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TEtranscripts
A package for including transposable elements in differential enrichment analysis of sequencing datasets.
http://hammelllab.labsites.cshl.edu/software/#TEtranscripts
GNU General Public License v3.0
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Reading the bam files
#143
MehdiM98
closed
10 months ago
9
View DE TE genes using IGV
#142
Sidy2015
closed
11 months ago
3
TE GTF format error! There is no annotation at line 1. Error in building TE index
#141
DangPengsanqi
closed
1 year ago
2
Error in building TE index with my TE.gtf file
#140
biomesser
closed
12 months ago
17
There are not enough reads to estimate fragment length.
#139
ghost
closed
1 year ago
6
Pre-generated TE GTF for GRCm39 Ensembl assembly
#138
kcwum
closed
1 year ago
2
TEcount:287 error
#137
dmnburrows
closed
1 year ago
3
Transposable elements have zero counts in .cntTable
#136
14stutzmanav
closed
1 year ago
16
AttributeError: 'Namespace' object has no attribute 'format'
#135
Dexter5577
closed
1 year ago
4
TEcount was killed after receiving the error: "Could not retrieve index file for '.1677762396.6834505.bam"
#134
Linran2023
closed
1 year ago
14
How to identify the Sequencing-GAP of a gene inserted by a transposon.
#133
Wenwen012345
closed
1 year ago
2
TEcount on multple BAMs
#132
cottrellka
closed
1 year ago
1
gtf used to generate pre-built index?
#131
EmersonH2
closed
1 year ago
2
Question about log2FoldChange and lfcSE
#130
jordana-olive
closed
1 year ago
3
How to deal with PCR duplication
#129
duzc-Repos
closed
1 year ago
2
TEtranscripts error after install
#128
Anna-xu408
closed
1 year ago
2
Generating pre-built gene and TE indexes for TEcount with TEtranscripts_indexer
#127
samuelruizperez
closed
1 year ago
3
T2T_refGene.gtf & T2T_rmsk_TE.gtf
#126
heeralvi
closed
1 year ago
3
outSAMmultNmax
#125
imerelli
closed
1 year ago
2
Saturation analysis for parameters in STAR
#124
kane9530
closed
1 year ago
2
TEtoolkit
#123
DanielaMombach
closed
1 year ago
6
How to consider the relationship between genes and TE when counting reads
#122
ZunpengLiu
closed
1 year ago
3
Fix for singularity issues
#121
molikd
closed
1 year ago
0
Singularity container derived from docker container misses DESeq2
#120
Rhinogradentia
closed
1 year ago
7
Singularity ERROR:root:No such file
#119
ferygood
closed
1 year ago
8
Generate pre-built index
#118
zhangaicen
closed
1 year ago
2
Feature request: specify output directory
#117
niekwit
closed
1 year ago
4
Removing whitespace, singularity documenation
#116
molikd
closed
1 year ago
0
.gitignore, workflows, and docker containers oh my!
#115
molikd
closed
1 year ago
0
Independent Filtering in R
#114
sanatbhadsavle
closed
1 year ago
2
generate custom GTF for new species
#113
MontseTor
closed
1 year ago
3
Error in building TE index
#112
zhangqc723
closed
1 year ago
6
requires argparse, a defunct library
#111
Apteryks
closed
1 year ago
2
Tiny differences for two identical BAM files (except for read headers)
#110
raquelgarza
closed
1 year ago
12
Error when using custom GTF file
#109
MariaRig
closed
2 years ago
2
count matrix contain >60000 genes, but only <1000 TE
#108
qiangfan2022
closed
2 years ago
9
Error with TE GFT while running TEtranscripts
#107
jpcartailler
closed
2 years ago
4
Intergenic TEs
#106
tiplud
closed
2 years ago
4
System requirements for TEtranscripts (locus level)
#105
olivertam
closed
2 years ago
2
TEcount processes multiple bam files at the same time
#104
shijiu001
closed
2 years ago
1
Creation of custom GTFs for TEs and how are solo Vs. full length TEs dealt with?
#103
milcs40
closed
1 year ago
22
dm6 TE GTF file
#102
MiaPaw
closed
2 years ago
1
Counts from TEtranscript STAR differ from previous quantification
#101
SBata
closed
2 years ago
3
source of Z. maize TE annotation
#100
kcamnairb
closed
2 years ago
2
Index name-sorted bam files.
#99
WeijiaSu
closed
2 years ago
1
Exception type: RuntimeError, raised in TEtranscripts:448
#98
ZeyanZhang
closed
2 years ago
8
TEtranscripts "Building TE index ......" Bus error
#97
ZeyanZhang
closed
2 years ago
2
GTF files for rice, also external index
#96
zhangaicen
closed
2 years ago
9
Error in building gene/TE index
#95
shenmeguimlf
closed
2 years ago
15
control samples
#94
amitpande74
closed
2 years ago
4
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