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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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If the BAM file is sorted by coordinates,please specify --sortByPos and re-run!
#161
SPRINNNGY
closed
11 months ago
14
No TE being quantified
#160
conery
closed
11 months ago
5
Error thrown when using paired end BAM
#159
Bessie92
closed
11 months ago
8
The question about TE disturbing with gene expression
#158
Wenwen012345
closed
11 months ago
6
Alignment Parameters
#157
bshim181
closed
12 months ago
2
quantify in the family level
#156
olivertam
closed
1 year ago
2
half of the reads are not annotated
#155
MonkeySylvia
closed
11 months ago
3
TE inconsistency
#154
ONAgaganb
closed
1 year ago
5
Using TEtranscripts on data from rare disease patients
#153
ChiaraF32
closed
1 year ago
2
Use the GFF3 format file to get the TE GTF format needed for TEtranscript
#152
ONAgaganb
closed
1 year ago
4
saturation analysis
#151
AlisaGU
closed
1 year ago
24
TEcount: does it count intronic TE?
#150
ddepierre
closed
1 year ago
4
How to exclude genes from out.cntTable OR extract counts for specific TE family
#149
farhan-lab
closed
1 year ago
11
single cell RNA-seq
#148
zhongguozhiwang
closed
1 year ago
5
chromatinRNA-seq compatibility
#147
max-biguet
closed
1 year ago
10
The problem with the strand.
#146
Wenwen012345
closed
1 year ago
4
TE GTF File Zero Counts
#145
BenjaMcM
closed
1 year ago
3
multiple core
#144
songlyzz
closed
1 year ago
2
Reading the bam files
#143
MehdiM98
closed
1 year ago
9
View DE TE genes using IGV
#142
Sidy2015
closed
1 year 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
1 year 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
2 years ago
2
Saturation analysis for parameters in STAR
#124
kane9530
closed
2 years ago
2
TEtoolkit
#123
DanielaMombach
closed
2 years ago
6
How to consider the relationship between genes and TE when counting reads
#122
ZunpengLiu
closed
2 years ago
3
Fix for singularity issues
#121
molikd
closed
2 years ago
0
Singularity container derived from docker container misses DESeq2
#120
Rhinogradentia
closed
2 years ago
7
Singularity ERROR:root:No such file
#119
ferygood
closed
2 years ago
8
Generate pre-built index
#118
zhangaicen
closed
2 years ago
2
Feature request: specify output directory
#117
niekwit
closed
2 years ago
4
Removing whitespace, singularity documenation
#116
molikd
closed
2 years ago
0
.gitignore, workflows, and docker containers oh my!
#115
molikd
closed
2 years ago
0
Independent Filtering in R
#114
sanatbhadsavle
closed
2 years ago
2
generate custom GTF for new species
#113
MontseTor
closed
2 years ago
3
Error in building TE index
#112
zhangqc723
closed
2 years ago
6
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