gpertea/stringtie

Issues

• pipeline:process_bams:stringtie (1) terminated with an error exit status (1)

  #441 opened 14 days ago by sme229
  0

• Support for gzip'd GTF input

  #440 opened 18 days ago by nick-youngblut
  0

• Stringtie2 segmentation fault

  #439 opened 21 days ago by YIGUIz
  0

• Stringtie2 segmentation fault

  #438 opened 21 days ago by YIGUIz
  0

• prepDE.py3 Error: could not locate transcript NM_011283 entry for sample A125

  #437 opened 22 days ago by Yu42698
  0

• Should I sort the merged BAM file after combining all the sorted BAM files?

  #436 opened 2 months ago by YIGUIz
  0

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

  #435 opened 2 months ago by erajshafiq
  0

• Change between 2.2.1 and 2.2.2 on gene abundance estimation with '-e' parameter

  #434 opened 2 months ago by lldelisle
  3

• Read length parameter for long reads using prepDE.py3

  #433 opened 2 months ago by dhrititandon
  0

• The output gtf file contains exon with coverage=0

  #432 opened 2 months ago by dudududu12138
  0

• Gene read count generated from prepDE.py for DESeq2 has duplicate genes

  #431 opened 2 months ago by FarzanehRah
  0

• Stuck on prepDE.py

  #427 opened 3 months ago by Kappy2
  2

• Merged genes on a de-novo assembly

  #429 opened 3 months ago by SalvadorGJ
  0

• Issue with reference annotation genes with identical coordinates

  #430 opened 3 months ago by N-Hoffmann
  0

• <class 'str'> with high reads after running prepDE.py3

  #403 opened a year ago by carlmed00
  2

• Discrepancy in counts extraction using prepDE.py3 with multiple samples in sample_list

  #428 opened 3 months ago by ruqinga
  0

• transcripts with identical coordinates but different abundances

  #426 opened 4 months ago by zjuezhen
  4

• Regions not covered by long read in --mix mode

  #425 opened 4 months ago by ytomofuji
  2

• The question for the inadequacy of transcripts

  #424 opened 4 months ago by CuteGold0407
  0

• Use of StringTie to assemby of unannotated intron retention transcripts

  #409 opened 10 months ago by CBenetti
  1

• How does stringtie process chimeric reads

  #423 opened 4 months ago by HelloYanming
  0

• Stringtie2 transcripts contain sequence from genome or reads mapped?

  #416 opened 4 months ago by sanyalab
  0

• Non-canonical splice sites in long-read data

  #422 opened 4 months ago by wenzelm
  0

• "Segmentation fault" Error using StringTie

  #394 opened a year ago by sen1019san
  2

• stringtie not responding to gff file

  #421 opened 4 months ago by Akashanil-akh
  0

• An error message in stringtie's mix option

  #420 opened 4 months ago by YIGUIz
  7

• Segmentation fault (core dumped) and problems of gene orientations

  #406 opened a year ago by Cesnl
  3

• Stringtie --mix returns "Error: the input alignment file is not sorted!" while short and long-reads alone are ok

  #419 opened 4 months ago by eggrandio
  3

• gtf was not generated with -e option

  #418 opened 5 months ago by Truman11Zeng
  0

• Assembled transcripts lack canonical transcript, clearly visible in the alignment

  #417 opened 6 months ago by mvheetve
  1

• StringTie --merge

  #402 opened a year ago by cc-prolix
  1

• Difference between read count from Star and stringtie

  #415 opened 7 months ago by giacuong171
  1

• How do I deal with this warning message?

  #414 opened 7 months ago by Kwon419
  0

• gene count value is zero; but TPM is not zero

  #413 opened 7 months ago by Niohuruzh
  0

• How to ignore strand information using strand-specific RNA-seq

  #412 opened 8 months ago by Starry-Sky-hu
  0

• Discrepancy in Quantification Results with and without -e Option

  #411 opened 8 months ago by HadoBoirudoWandarando
  0

• stringtie mix option

  #410 opened 10 months ago by anuradhareddi
  0

• input file format

  #408 opened a year ago by dvirdi01
  0

• how do you get all the potential processed transcripts

  #407 opened a year ago by pcantalupo
  1

• Stringtie --merge -c

  #405 opened a year ago by SEVEN-XYCHEN
  0

• problem with python prepDE.py3 -i sample_lst.txt

  #404 opened a year ago by danielpovedam
  1

• Whether stringtie will include novel transcripts into ballgown file? What other tools can be used to visualize novel transcripts?

  #401 opened a year ago by guodudou2
  0

• I wonder 'else' clause should be commented out (or deleted) in prepDE.py3, in the block of badGenes check

  #400 opened a year ago by mickeykawai
  0

• Not compiling SuperReads_RNA

  #399 opened a year ago by rafaeltiveron
  1

• StringTie for single-end reads

  #398 opened a year ago by Mirror1211
  1

• Error when running prepDE.py

  #396 opened a year ago by chickenHyop
  1

• Springtie installation instructions fail on "make release"

  #397 opened a year ago by nvannest
  0

• Segmentation Error with Stringtie mix. The bundle appears too large.

  #395 opened a year ago by niradsp
  0

• "Segmentation fault" error

  #393 opened a year ago by sen1019san
  0

• "The -c and -m parameters of StringTie are not effective.

  #392 opened a year ago by tongtongy666
  3