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gpertea
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stringtie
Transcript assembly and quantification for RNA-Seq
MIT License
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StringTie --merge
#402
cc-prolix
opened
1 year ago
1
Whether stringtie will include novel transcripts into ballgown file? What other tools can be used to visualize novel transcripts?
#401
guodudou2
opened
1 year ago
0
I wonder 'else' clause should be commented out (or deleted) in prepDE.py3, in the block of badGenes check
#400
mickeykawai
opened
1 year ago
0
Not compiling SuperReads_RNA
#399
rafaeltiveron
opened
1 year ago
1
StringTie for single-end reads
#398
Mirror1211
closed
1 year ago
1
Springtie installation instructions fail on "make release"
#397
nvannest
opened
1 year ago
0
Error when running prepDE.py
#396
chickenHyop
closed
1 year ago
1
Segmentation Error with Stringtie mix. The bundle appears too large.
#395
niradsp
opened
1 year ago
0
"Segmentation fault" Error using StringTie
#394
sen1019san
closed
1 year ago
2
"Segmentation fault" error
#393
sen1019san
opened
1 year ago
0
"The -c and -m parameters of StringTie are not effective.
#392
tongtongy666
opened
1 year ago
3
when dealing with big genomes, the error occurs: "the input alignment file is not sorted!"
#391
dujuanhua6308
opened
1 year ago
3
Segmentation fault only in "-mix" mode.
#390
fangbohao
opened
1 year ago
0
Segmentation fault 11
#389
theokirkland
opened
1 year ago
6
Some problem with Stringtie prepDE.py
#388
Nong510673
opened
1 year ago
1
Issue: PrepDE.py Script "IndexError: list index out of range"
#387
mlvanhorn
opened
1 year ago
1
Recommendations for calling StringTie with RNA-seq data from small-genome organisms such as S. cerevisiae
#386
kalavattam
opened
1 year ago
0
bugfix: Allow updating -s
#385
kdm9
opened
1 year ago
0
Stringtie not identifying unannotated exon (annotated or de novo assembly)
#384
dmworstell
opened
2 years ago
1
A new transcript appears after stringtie2 --merge used
#383
Hubuyan
opened
2 years ago
0
One gene outputs multiple TPM values
#382
HengkuanLi
opened
2 years ago
3
Issue: could not locate transcript gene
#381
carlmed00
opened
2 years ago
1
StringTie gives incorrect 5 end.
#380
Pentayouth
opened
2 years ago
0
Coverage in output gif file
#379
AyushSemwal
opened
2 years ago
0
stringtie recognizes and converts CDS?
#378
choiseungji
opened
2 years ago
1
fix some building warning
#377
kkzhsh
opened
2 years ago
1
Stringtie skips pseudo genes from reference gtf
#376
m-waqas
opened
2 years ago
0
Stringtie skips some reference gene ids
#375
m-waqas
closed
2 years ago
0
gene/transcript abundance
#374
woshiyangsi
opened
2 years ago
0
Duplication of an exon is consider as an insertion
#373
Nedss
opened
2 years ago
0
How to retain genomic coordinates (chr, start, end, strand) of genes when going from StringTie to Ballgown or DESeq2?
#372
kainth-amoldeep
opened
2 years ago
0
fix #348 . Adds mutex to manage concurrent writing to covered referen…
#371
gsatas
closed
2 years ago
1
There is a case where the 5' side of Exon disappears in StringTie merge
#370
c2997108
opened
2 years ago
0
LongReads.fq is empty and superReadSequences.fasta looks like longreads
#368
Evenlyeven
opened
2 years ago
0
How do I run if I have Illumina, Nanopore AND PacBio data?
#367
niradsp
opened
2 years ago
0
Can stringtie count partially transcribed transcripts into gene counts?
#366
quwei00
opened
2 years ago
0
FPKM filter in stringtie --merge
#365
pasviber
opened
2 years ago
0
Overlapped gene ids in the gene abundance tab file
#363
dahun73
closed
2 years ago
0
Please consider making dependencies able to be dynamically linked
#362
SethosII
opened
2 years ago
2
Error: no valid ID found for GFF record
#361
zuodabin
opened
2 years ago
2
prepDE.py error: sample file not generated by -e option
#360
zjj19910
closed
2 years ago
2
Segmentation Fault when merge scallop2 gtfs
#359
xiekunwhy
opened
2 years ago
1
--mix with -e loses guide transcripts
#358
gpertea
opened
2 years ago
1
duplicate transcript output with -L -e
#357
AmrSaadeldin
opened
2 years ago
5
segmentation fault with long read data [ stringtie v2.2.1 ]
#356
zhixue
closed
2 years ago
7
error:discarding overlapping duplicate gene feature during assembly process
#355
ravisaroch
closed
2 years ago
0
Multiple transcripts with the same coordinates
#354
suyeonwy
opened
2 years ago
0
StringTie is unable to predict known transcripts.
#353
unique379r
opened
2 years ago
0
stringtie/2.0.3 ignoring reads
#352
zhezhenwang
opened
2 years ago
0
How to filter the merged transcripts
#351
Huangyizhong
opened
2 years ago
6
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