gpertea stringtie issues

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq

MIT License

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issues

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which output file contains identified novel exons in stringtie/2.2.1 ?

#435 erajshafiq opened 1 week ago
0
Change between 2.2.1 and 2.2.2 on gene abundance estimation with '-e' parameter

#434 lldelisle opened 2 weeks ago
3
Read length parameter for long reads using prepDE.py3

#433 dhrititandon opened 2 weeks ago
0
The output gtf file contains exon with coverage=0

#432 dudududu12138 opened 2 weeks ago
0
Gene read count generated from prepDE.py for DESeq2 has duplicate genes

#431 FarzanehRah opened 3 weeks ago
0
Issue with reference annotation genes with identical coordinates

#430 N-Hoffmann opened 1 month ago
0
Merged genes on a de-novo assembly

#429 SalvadorGJ opened 1 month ago
0
Discrepancy in counts extraction using prepDE.py3 with multiple samples in sample_list

#428 ruqinga opened 1 month ago
0
Stuck on prepDE.py

#427 Kappy2 closed 1 month ago
2
transcripts with identical coordinates but different abundances

#426 zjuezhen opened 2 months ago
4
Regions not covered by long read in --mix mode

#425 ytomofuji closed 2 months ago
2
The question for the inadequacy of transcripts

#424 CuteGold0407 opened 2 months ago
0
How does stringtie process chimeric reads

#423 HelloYanming opened 2 months ago
0
Non-canonical splice sites in long-read data

#422 wenzelm opened 2 months ago
0
stringtie not responding to gff file

#421 Akashanil-akh opened 2 months ago
0
An error message in stringtie's mix option

#420 YIGUIz opened 2 months ago
7
Stringtie --mix returns "Error: the input alignment file is not sorted!" while short and long-reads alone are ok

#419 eggrandio closed 2 months ago
3
gtf was not generated with -e option

#418 Truman11Zeng opened 3 months ago
0
Assembled transcripts lack canonical transcript, clearly visible in the alignment

#417 mvheetve opened 4 months ago
1
Stringtie2 transcripts contain sequence from genome or reads mapped?

#416 sanyalab closed 2 months ago
0
Difference between read count from Star and stringtie

#415 giacuong171 opened 5 months ago
1
How do I deal with this warning message?

#414 Kwon419 opened 5 months ago
0
gene count value is zero; but TPM is not zero

#413 Niohuruzh opened 5 months ago
0
How to ignore strand information using strand-specific RNA-seq

#412 Starry-Sky-hu opened 6 months ago
0
Discrepancy in Quantification Results with and without -e Option

#411 HadoBoirudoWandarando opened 6 months ago
0
stringtie mix option

#410 anuradhareddi opened 8 months ago
0
Use of StringTie to assemby of unannotated intron retention transcripts

#409 CBenetti opened 8 months ago
1
input file format

#408 dvirdi01 opened 9 months ago
0
how do you get all the potential processed transcripts

#407 pcantalupo opened 9 months ago
1
Segmentation fault (core dumped) and problems of gene orientations

#406 Cesnl opened 9 months ago
3
Stringtie --merge -c

#405 SEVEN-XYCHEN opened 9 months ago
0
problem with python prepDE.py3 -i sample_lst.txt

#404 danielpovedam closed 11 months ago
1
<class 'str'> with high reads after running prepDE.py3

#403 carlmed00 opened 1 year ago
2
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