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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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control samples
#94
amitpande74
closed
2 years ago
4
GTF issue
#93
singharchana23
closed
2 years ago
2
counts for individual Transcripts of TE gene
#92
yingyin2019
closed
2 years ago
1
GTF files for macaques, bonobo, and also external index
#91
ferygood
closed
2 years ago
2
Personal GTF file error
#90
AlBaarS
closed
3 years ago
3
Error in EM step due to GTF
#89
pillailab
closed
3 years ago
4
error
#88
amitpande74
closed
3 years ago
3
running TEcount with external indexes
#87
retrogenomics
closed
3 years ago
27
error while running TE counts
#86
amitpande74
closed
3 years ago
2
output TE_analysis with ENSMUS codes
#85
JihedC
closed
3 years ago
2
Count output for paired end reads
#84
emattei
closed
3 years ago
2
Making TE.gtf using Genome.fa.out file made by RepeatMasker?
#83
wangshun1121
closed
1 year ago
8
Could not retrieve index file for '.1606144755.39.bam'
#82
kennethchenlab
closed
3 years ago
10
Counting TEs in introns
#81
mlizio
closed
1 year ago
3
TEcount can be run on multiple BAM files?
#80
my0916
closed
3 years ago
2
Majority of TE reads coming from Chomosome 1 with human data
#79
rowancallahan
closed
3 years ago
2
Question about the hg19_rmsk.vcf file
#78
xunchen85
closed
3 years ago
2
Question about use a subset of TE for quantification withTEtranscripts
#77
Meowth-3Dchr
closed
3 years ago
5
TECount counting/assignment of 'split reads' to features
#76
lfra
closed
3 years ago
4
Difference between provided TE GTF and TE GTF made from UCSC tracks by makeTEgtf.pl
#75
XinyuXiang
closed
3 years ago
4
No .txt output files
#74
maureenwidyawan
closed
3 years ago
9
--verbose command line parsing
#73
wresch
closed
3 years ago
2
0 count for TEs in all samples
#72
HannahDixon
closed
4 years ago
3
TEtranscripts stopped at TE index building step
#71
hugch2020
closed
4 years ago
2
What kind of data does control sample needed and question about personal GTF?
#70
Jiaqichen1202
closed
1 year ago
26
-outFilterMultimapNmax bigger than winAnchorMultimapNmax
#69
RRebo
closed
4 years ago
1
Using a GFF3 for alignment
#68
r-mashoodh
closed
4 years ago
7
Error for differential expression analysis
#67
BenjaminSchwessinger
closed
4 years ago
5
Request for a small test dataset
#66
stephanflemming
closed
4 years ago
15
Intronic TEs
#65
jentiger82
closed
4 years ago
3
how to deal with duplicates in data from RNA-seq or scRNA-seq?
#64
AIBio
closed
4 years ago
2
details about making GTF file for TEtranscripts
#63
AIBio
closed
4 years ago
2
Not counting genes
#62
tonilogbo
closed
4 years ago
10
Python 3?
#61
dpryan79
closed
3 years ago
6
TEcount and 10X Genomics single Cell data support?
#60
SolKatzman
closed
4 years ago
1
TE_rmsk gtf file has multiple family_id or class_id for gene_id items
#59
SolKatzman
closed
3 years ago
9
standalone command for TEindex ?
#58
SolKatzman
closed
4 years ago
8
Error in building gene/TE index
#57
alp78
closed
4 years ago
6
Finding as much as 68% of reads originating from TE elements?
#56
aleighbrown
closed
4 years ago
3
Problem with R processing
#55
alp78
closed
4 years ago
2
Memory requirements + threading
#54
aleighbrown
closed
4 years ago
1
Error in building TE index with TEcount
#53
iaval
closed
4 years ago
4
Error in building gene/TE index on linux machine , installed with pip
#52
aleighbrown
closed
4 years ago
8
Input with STAR aligned and chimeric BAM files?
#51
evanwangx
closed
4 years ago
3
Double Checking Strandedness Flag Meaning
#50
jimcdonald
closed
4 years ago
2
Counting read problems + extract sequences & genomic positions for specific TEs
#49
lfra
closed
4 years ago
10
--stranded option
#48
clouds-drift
closed
4 years ago
4
a question about the teloolkit input gff3 file
#47
ChenDepp
closed
4 years ago
8
Read-counting with TEcount - low counts
#46
lfra
closed
4 years ago
3
Failure to recognize sorted ATACseq BAM file
#45
dango147
closed
4 years ago
4
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