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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Error in building gene/TE index

#192 77CXiao closed 1 day 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 1 week 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 1 week 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 4 months ago
1
TE annotation for Rabbit (oryCun2)

#174 hiskobay closed 3 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 6 months ago
6
Alignment Parameters

#157 bshim181 closed 6 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 8 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 7 months ago
5
chromatinRNA-seq compatibility

#147 max-biguet closed 9 months ago
10
The problem with the strand.

#146 Wenwen012345 closed 10 months ago
4
TE GTF File Zero Counts

#145 BenjaMcM closed 9 months ago
3
multiple core

#144 songlyzz closed 10 months ago
2
Reading the bam files

#143 MehdiM98 closed 10 months ago
9