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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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STAR parameters prior to TE quantification
#194
albertozenere
opened
1 day ago
3
Losing many reads after quantification with TEcount
#193
sanhe374
closed
1 day ago
8
Error in building gene/TE index
#192
77CXiao
closed
5 days ago
9
pkg_resources.DistributionNotFound
#191
GimenaA
opened
2 weeks ago
1
SamtoolsError
#190
ikaufhold
closed
2 weeks ago
2
TEcount: Issue - There are not enough reads to estimate fragment length.
#189
MichMourra
closed
2 weeks ago
4
Ask about the error message and the problem of networking: Reason: Couldn't connect to server
#188
l1y1y
opened
1 month ago
10
Inquire about the suitability of TEtranscripts for long-read RNA-Seq analysis
#187
evayfang2019
closed
2 weeks ago
3
Understanding count matrix discrepancies and exploring transcript-level differential expression with TEcount/TEtranscripts
#186
ptranvan
closed
1 month ago
6
[E::idx_find_and_load] Could not retrieve index file for '.1712579023.8525763.bam'
#185
ptranvan
closed
2 months ago
6
basic questions about TEtranscripts
#184
shaymin84
closed
1 month ago
32
Very low basemeans compared to another pipeline
#183
murphytho
closed
2 months ago
14
prepare the GTF file for wheat(IWGSC RefSeq v1.1)
#182
wj0922
closed
2 months ago
2
OSError, raised in libcalignmentfile.pyx:1876
#181
zhaoj81
closed
4 months ago
2
TE GTF format error
#180
conery
closed
4 months ago
6
Calculate TE's CPM expression frequency
#179
songlyzz
closed
3 months ago
7
Consistently higher TE expression in control rather than treatment across many datasets
#178
stevencincotta
closed
3 months ago
4
TElocal to locate the TE loci
#177
songlyzz
closed
5 months ago
1
TE subfamily TPM nomalize
#176
songlyzz
closed
4 months ago
3
TEcount killed
#175
sanhe374
closed
5 months ago
1
TE annotation for Rabbit (oryCun2)
#174
hiskobay
closed
4 months ago
3
GTF annotation to use for TE
#173
sanhe374
closed
5 months ago
2
Error: malformatted header: no ':' in field
#172
fanghe0720
closed
4 months ago
6
Strandedness of TEs and getting antisense counts
#171
murphytho
closed
4 months ago
10
All ERV genes have high reads in tumor
#170
frankligy
closed
5 months ago
3
Results Gene counts total 0.0 Total annotated reads = 0
#169
paulineBazelle
closed
5 months ago
6
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated. E::bgzf_read] bgzf_read_block error -1 after 0 of 4 bytes-ERROR when reading sample BAM files
#168
yahanlian
closed
5 months ago
7
Error building TE index
#167
xxu092
closed
5 months ago
10
mapping gtf version different with TEtranscripts version
#166
songlyzz
closed
5 months ago
3
Input file
#165
LIUXING-bio
closed
5 months ago
7
Question on output table
#164
Drosofriends
closed
5 months ago
6
The issue of slow running speed of TEtranscripts
#163
cyyisbest
closed
7 months ago
2
Extract specific type of Transposable Element (TE)reads
#162
sixingchen718
closed
6 months ago
3
If the BAM file is sorted by coordinates,please specify --sortByPos and re-run!
#161
SPRINNNGY
closed
6 months ago
14
No TE being quantified
#160
conery
closed
6 months ago
5
Error thrown when using paired end BAM
#159
Bessie92
closed
6 months ago
8
The question about TE disturbing with gene expression
#158
Wenwen012345
closed
7 months ago
6
Alignment Parameters
#157
bshim181
closed
7 months ago
2
quantify in the family level
#156
olivertam
closed
7 months ago
2
half of the reads are not annotated
#155
MonkeySylvia
closed
6 months ago
3
TE inconsistency
#154
ONAgaganb
closed
7 months ago
5
Using TEtranscripts on data from rare disease patients
#153
ChiaraF32
closed
7 months ago
2
Use the GFF3 format file to get the TE GTF format needed for TEtranscript
#152
ONAgaganb
closed
7 months ago
4
saturation analysis
#151
AlisaGU
closed
9 months ago
24
TEcount: does it count intronic TE?
#150
ddepierre
closed
9 months ago
4
How to exclude genes from out.cntTable OR extract counts for specific TE family
#149
farhan-lab
closed
9 months ago
11
single cell RNA-seq
#148
zhongguozhiwang
closed
8 months ago
5
chromatinRNA-seq compatibility
#147
max-biguet
closed
9 months ago
10
The problem with the strand.
#146
Wenwen012345
closed
11 months ago
4
TE GTF File Zero Counts
#145
BenjaMcM
closed
10 months ago
3
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