mhammell-laboratory TEtranscripts issues

mhammell-laboratory / 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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issues

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No module named setuptools

#211 GimenaA opened 1 day ago
5
TE sequence Issue

#210 Jinloong-dream opened 1 day ago
1
TE GTF for non-model species

#209 canyon-hub opened 2 weeks ago
3
Differences between featureCounts and TEtranscripts results

#208 CSU-KangHu opened 2 weeks ago
1
Could not retrieve index file When I run the TEtranscripts though I deal with Gene and TE gtf

#207 1228849000 opened 2 weeks ago
2
TEcount Pause for a long time at the TE index building stage

#206 iriirica closed 3 weeks ago
4
TE GTF format error

#205 Kkk-2001 opened 1 month ago
16
locating TEs, esp. in Retained Introns (RI)

#204 tud03125 closed 1 week ago
10
Which sequence search engine do you recommend for best comparison with your curated GTF files?

#203 jacel closed 1 month ago
2
Does TEtranscripts support Windows?

#202 Ranxuqing closed 1 month ago
3
Error in building TE index

#201 jsnoliva closed 3 weeks ago
8
Question: Gene count being 0 in TEtranscripts Output

#200 vivi-1406 closed 2 months ago
3
Error: TE_anno.gtf

#199 dtx282000 closed 2 months ago
3
Error: Hangup

#198 dtx282000 closed 2 months ago
16
Upload the TE_GTF of Capra hircus

#197 LindaMax001 closed 2 months ago
3
Question: different Genes/TEs expression

#196 zhangqc723 closed 2 months ago
3
full-length L1

#195 BenxiaHu closed 3 months ago
5
STAR parameters prior to TE quantification

#194 albertozenere closed 4 months ago
4
Losing many reads after quantification with TEcount

#193 sanhe374 closed 4 months ago
8
Error in building gene/TE index

#192 77CXiao closed 4 months ago
9
pkg_resources.DistributionNotFound

#191 GimenaA closed 4 months ago
2
SamtoolsError

#190 ikaufhold closed 5 months ago
2
TEcount: Issue - There are not enough reads to estimate fragment length.

#189 MichMourra closed 5 months ago
4
Ask about the error message and the problem of networking： Reason: Couldn't connect to server

#188 l1y1y closed 4 months ago
11
Inquire about the suitability of TEtranscripts for long-read RNA-Seq analysis

#187 evayfang2019 closed 5 months ago
3
Understanding count matrix discrepancies and exploring transcript-level differential expression with TEcount/TEtranscripts

#186 ptranvan closed 6 months ago
8
[E::idx_find_and_load] Could not retrieve index file for '.1712579023.8525763.bam'

#185 ptranvan closed 7 months ago
14
basic questions about TEtranscripts

#184 shaymin84 closed 6 months ago
32
Very low basemeans compared to another pipeline

#183 murphytho closed 7 months ago
14
prepare the GTF file for wheat（IWGSC RefSeq v1.1）

#182 wj0922 closed 7 months ago
2
OSError, raised in libcalignmentfile.pyx:1876

#181 zhaoj81 closed 9 months ago
2
TE GTF format error

#180 conery closed 9 months ago
6
Calculate TE's CPM expression frequency

#179 songlyzz closed 8 months ago
7
Consistently higher TE expression in control rather than treatment across many datasets

#178 stevencincotta closed 8 months ago
4
TElocal to locate the TE loci

#177 songlyzz closed 9 months ago
1
TE subfamily TPM nomalize

#176 songlyzz closed 9 months ago
3
TEcount killed

#175 sanhe374 closed 9 months ago
1
TE annotation for Rabbit (oryCun2)

#174 hiskobay closed 8 months ago
3
GTF annotation to use for TE

#173 sanhe374 closed 10 months ago
2
Error: malformatted header: no ':' in field

#172 fanghe0720 closed 9 months ago
6
Strandedness of TEs and getting antisense counts

#171 murphytho closed 9 months ago
10
All ERV genes have high reads in tumor

#170 frankligy closed 10 months ago
3
Results Gene counts total 0.0 Total annotated reads = 0

#169 paulineBazelle closed 10 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 10 months ago
7
Error building TE index

#167 xxu092 closed 10 months ago
10
mapping gtf version different with TEtranscripts version

#166 songlyzz closed 10 months ago
3
Input file

#165 LIUXING-bio closed 10 months ago
7
Question on output table

#164 Drosofriends closed 10 months ago
6
The issue of slow running speed of TEtranscripts

#163 cyyisbest closed 12 months ago
2
Extract specific type of Transposable Element (TE)reads

#162 sixingchen718 closed 11 months ago
3