gpertea stringtie issues

gpertea / stringtie

Transcript assembly and quantification for RNA-Seq

MIT License

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How to quantify lncRNA using strintgie？

#452 qingzengLi opened 4 days ago
1
Error: could not locate transcript ENST00000472017.1

#451 Upreti-Anil opened 1 week ago
0
Is XS tag still required when strandedness is given as a parameter?

#450 weishwu opened 2 weeks ago
0
Latest GTF version compatibility

#449 pratibha-bioinfo opened 4 weeks ago
0
Getting error with StringTie

#448 YIGUIz opened 1 month ago
0
stringtie halts at a bundle that have large number of alignments and junctions

#447 husensofteng opened 1 month ago
4
single exon transcripts missing strand information

#446 YIGUIz closed 1 month ago
0
PrepDE giving 'duplicate' count data

#445 pmccusker09 opened 2 months ago
0
Getting error with StringTie

#444 nayan-bhowmik opened 3 months ago
1
Update xz source link

#443 Dreista closed 3 months ago
2
Paired-end reads: is superreads required? And how to use superreads if MaSuRCA is installed using bioconda?

#442 PVlasov93 opened 3 months ago
2
pipeline:process_bams:stringtie (1) terminated with an error exit status (1)

#441 sme229 opened 3 months ago
0
Support for gzip'd GTF input

#440 nick-youngblut opened 3 months ago
0
Stringtie2 segmentation fault

#439 YIGUIz opened 3 months ago
0
Stringtie2 segmentation fault

#438 YIGUIz closed 3 months ago
0
prepDE.py3 Error: could not locate transcript NM_011283 entry for sample A125

#437 Yu42698 opened 3 months ago
0
Should I sort the merged BAM file after combining all the sorted BAM files?

#436 YIGUIz opened 4 months ago
0
which output file contains identified novel exons in stringtie/2.2.1 ?

#435 erajshafiq opened 4 months ago
0
Change between 2.2.1 and 2.2.2 on gene abundance estimation with '-e' parameter

#434 lldelisle opened 5 months ago
3
Read length parameter for long reads using prepDE.py3

#433 dhrititandon opened 5 months ago
0
The output gtf file contains exon with coverage=0

#432 dudududu12138 opened 5 months ago
0
Gene read count generated from prepDE.py for DESeq2 has duplicate genes

#431 FarzanehRah opened 5 months ago
0
Issue with reference annotation genes with identical coordinates

#430 N-Hoffmann opened 5 months ago
0
Merged genes on a de-novo assembly

#429 SalvadorGJ opened 5 months ago
0
Discrepancy in counts extraction using prepDE.py3 with multiple samples in sample_list

#428 ruqinga opened 6 months ago
0
Stuck on prepDE.py

#427 Kappy2 closed 6 months ago
2
transcripts with identical coordinates but different abundances

#426 zjuezhen opened 6 months ago
4
Regions not covered by long read in --mix mode

#425 ytomofuji closed 6 months ago
2
The question for the inadequacy of transcripts

#424 CuteGold0407 opened 6 months ago
0
How does stringtie process chimeric reads

#423 HelloYanming opened 6 months ago
0
Non-canonical splice sites in long-read data

#422 wenzelm opened 6 months ago
0
stringtie not responding to gff file

#421 Akashanil-akh opened 6 months ago
0
An error message in stringtie's mix option

#420 YIGUIz opened 7 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 7 months ago
3
gtf was not generated with -e option

#418 Truman11Zeng opened 8 months ago
0
Assembled transcripts lack canonical transcript, clearly visible in the alignment

#417 mvheetve opened 9 months ago
1
Stringtie2 transcripts contain sequence from genome or reads mapped?

#416 sanyalab closed 6 months ago
0
Difference between read count from Star and stringtie

#415 giacuong171 opened 9 months ago
1
How do I deal with this warning message?

#414 Kwon419 opened 10 months ago
0
gene count value is zero; but TPM is not zero

#413 Niohuruzh opened 10 months ago
0
How to ignore strand information using strand-specific RNA-seq

#412 Starry-Sky-hu opened 11 months ago
0
Discrepancy in Quantification Results with and without -e Option

#411 HadoBoirudoWandarando opened 11 months ago
0
stringtie mix option

#410 anuradhareddi opened 1 year ago
0
Use of StringTie to assemby of unannotated intron retention transcripts

#409 CBenetti opened 1 year ago
1
input file format

#408 dvirdi01 opened 1 year ago
0
how do you get all the potential processed transcripts

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

#406 Cesnl opened 1 year ago
3
Stringtie --merge -c

#405 SEVEN-XYCHEN opened 1 year ago
0
problem with python prepDE.py3 -i sample_lst.txt

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

#403 carlmed00 opened 1 year ago
2