bioinfo-biols/CIRIquant

Issues

• Some questions about the results of ciriquant

  #72 opened 3 months ago by mysolid23
  0

• I used the parameter --bed with circAtlas bed file, the outputs are always "KeyError: '[circAtlas ID]'"

  #70 opened 5 months ago by DooYal
  3

• install CIRIquant using the recommend way

  #69 opened 6 months ago by mysolid23
  0

• invalid syntax in hisat2_read_statistics.py

  #67 opened 7 months ago by qj009
  0

• HISAT2 is not working as expected

  #66 opened 9 months ago by guillepl
  0

• hisat2-build index for circRNA-seq

  #65 opened 9 months ago by fengweimin-maker
  3

• Error in 'Detecting FSJ reads from genome alignment file'

  #40 opened 2 years ago by stefanerb89
  2

• HISAT2 Error: Encountered internal HISAT2 exception (#1）

  #64 opened 10 months ago by EdWardYF7
  1

• Hisat2 produces empty bam files

  #63 opened a year ago by Braulium
  0

• .fa is empty, index does not exist

  #35 opened 3 years ago by algaebrown
  4

• How to get the p-value from DE analysis?

  #62 opened a year ago by Li-Chengyu
  0

• Issue with EdgeR Installation in CIRIquant

  #59 opened a year ago by gkibt
  11

• sample_index does not exist Exiting now

  #61 opened a year ago by Yonglee1
  3

• Question: Predict circRNAs using multiple tools

  #60 opened a year ago by farzamani
  1

• KeyError

  #58 opened a year ago by stefanerb89
  0

• CIRIquant for stranded paired-end reads(dUTP method)

  #57 opened a year ago by junjunlab
  1

• Error in prepDE.py

  #55 opened 2 years ago by chickenHyop
  4

• Alignment does not end

  #54 opened 2 years ago by kendaida
  0

• full-length sequence of circRNA

  #53 opened 2 years ago by Zheng19w
  3

• multiple fastq files

  #52 opened 2 years ago by sung
  1

• Error while running CIRIquant

  #50 opened 2 years ago by nandakumaryellapu
  7

• Limitation on Number of Samples Used/DE Filtering Issue?

  #51 opened 2 years ago by mlvanhorn
  1

• A question about the results of differential expression analysis

  #49 opened 2 years ago by abedkurdi
  0

• ValueError: file header is empty (mode='rb') - is it SAM/BAM format?

  #48 opened 2 years ago by choijamtsmunkhzul
  0

• Problem with installation of CIRIquant

  #47 opened 2 years ago by choijamtsmunkhzul
  0

• Deferentially expressed circRNAs with biological replicate

  #45 opened 2 years ago by ravisaroch
  1

• Small gtf file issue

  #46 opened 2 years ago by Mathan98
  0

• How to measure whether circRNAs are significantly different

  #43 opened 2 years ago by litao1503
  0

• IOError: [Errno 2] No such file or directory: '/mnt/f/liu-project/lncRNA-mRNA-circRNA/5.circRNA-data/quant-data/circ/test.ciri'

  #42 opened 2 years ago by junjunlab
  1

• Can CIRI_DE_replicate be used for Differential expression analysis of DS_score

  #41 opened 2 years ago by tjhwangxiong
  3

• .log show successful completion, but there is no file

  #38 opened 3 years ago by algaebrown
  3

• Cannot split into 12 (16) pieces with size of 6246233965 and named them as /oasis/tscc/scratch/hsher/circSTAMP_pipe/output/circ/APO-noD-R_unmapped.sam. Fatal error. Aborted.

  #37 opened 3 years ago by algaebrown
  2

• change the permissions on 'CIRI2.pl' while running CIRIquant on cluster

  #36 opened 3 years ago by MaryamLabaf
  3

• Very low numbers for circular RNAs

  #34 opened 3 years ago by FerallOut
  3

• About CircAtlas sequence length

  #33 opened 3 years ago by andre-gabriel-42
  4

• Issue running prepDE.py

  #32 opened 4 years ago by G-Molano-LA
  3

• Encountered internal HISAT2 exception (#1)

  #31 opened 4 years ago by cjs0617
  8

• Issue with using find_circ prediction results for CIRIquant

  #30 opened 4 years ago by prisca399
  1

• Can CIRIquant be used with single-end data?

  #19 opened 4 years ago by stiv1n
  3

• Question regarding RNaseR corretion

  #16 opened 4 years ago by baylorbiostat
  1

• why miss so many circRNA to putout ?

  #18 opened 4 years ago by gnilihzeux
  8

• Generate empty gtf file

  #29 opened 4 years ago by mrb20045
  10

• About BSJs and FSJs

  #28 opened 4 years ago by andre-gabriel-42
  2

• EdgeR in CIRI_DE_replicate issue

  #26 opened 4 years ago by andre-gabriel-42
  7

• Different circRNA prediction tools for differential expression

  #22 opened 4 years ago by prisca399
  4

• Not able to generate the final circ.gtf output

  #24 opened 4 years ago by eltonjrv
  4

• duplicate rows R error in CIRI_DE_replicate

  #25 opened 4 years ago by eltonjrv
  5

• Read count cut-off for circRNA differential expression

  #21 opened 4 years ago by prisca399
  6

• Rowname error with CIRI_DE_replicate command

  #23 opened 4 years ago by prisca399
  2

• KeyError: 'chr1_89476615_89476806'

  #17 opened 4 years ago by gnilihzeux
  3