getzlab/rnaseqc

Issues

• Exon_reads.gct.gz file raw count data are not integer

  #88 opened 19 days ago by zhangpicb
  4

• Unique rate of mapped=1, duplicate rate of mapped=0, estimated library complexity =0 on test_data provided

  #87 opened 4 months ago by RnaSeqGal
  0

• "Total Reads" misleading, how to get the input read count?

  #85 opened 8 months ago by gpertea
  2

• So difficult to prepare a gtf for rnaseqc

  #81 opened a year ago by xiekunwhy
  7

• install issues

  #72 opened 2 years ago by rohan-bareja-turnstone
  2

• in the output *.metrics.tsv file, many metrics are 0/-nan

  #37 opened 5 years ago by AlvinZuo
  26

• collapse_annotation.py cannot process the gtf file generated by gffread

  #71 opened 2 years ago by biozzq
  2

• "Cannot compute median of an empty list" after reducing --gene-length to 1

  #84 opened a year ago by js72587
  0

• RNASeqc workflows erroring out (when a sample has no reads mapped?)

  #83 opened a year ago by matren395
  0

• More 5'/3' bias edge cases

  #79 opened a year ago by kachulis
  1

• "Expression Profiling Efficiency" description in Metrics.md

  #76 opened 2 years ago by paulimer
  2

• Uniquely Mapping Reads are overestimated

  #80 opened a year ago by Rohit-Satyam
  1

• Faulty estimates of Read Length

  #77 opened 2 years ago by karl-az
  1

• Alternative to collapse transcripts

  #31 opened 5 years ago by adomingues
  12

• Error when running rnaseqc with non-standard gtf annotation file

  #75 opened 2 years ago by magmir71
  1

• 5'/3' bias edge case bugs

  #74 opened 2 years ago by kachulis
  1

• rnaseqc v2.4.2 unable to parse collapsed genes GTF

  #73 opened 2 years ago by limrock1
  2

• Issue with creating a jupyter notebook

  #68 opened 2 years ago by NomiCentarix
  3

• mapping quality argument

  #69 opened 2 years ago by NomiCentarix
  1

• Collapse.py file

  #47 opened 2 years ago by jjyotikataria
  6

• Why 3' bias ratio is less than 0.5?

  #64 opened 2 years ago by y9c
  1

• rRNA rate difference in new version.

  #62 opened 2 years ago by bishwaG
  1

• How can I generate the figure reflecting the coverage over the gene body?

  #70 opened 2 years ago by biozzq
  1

• 0-counts for all genes

  #67 opened 2 years ago by NomiCentarix
  3

• installation problem

  #66 opened 2 years ago by NomiCentarix
  1

• library type

  #65 opened 2 years ago by leungman426
  1

• Failed to parse GTF: non-unique Exon ID

  #34 opened 4 years ago by bsmith030465
  27

• Strand argument clarification

  #59 opened 3 years ago by cmatKhan
  2

• Genes have "0" coverage in sample.coverage.tsv but definitely not 0 in sample.exon_reads.gct

  #61 opened 3 years ago by jiaan-yu
  2

• "Duplicate Reads" metric not calculated, always outputs 0.

  #60 opened 3 years ago by kachulis
  1

• Closed alignment block end coordinate comparison

  #57 opened 3 years ago by zeus19900814
  1

• Installation Error

  #58 opened 3 years ago by cmatKhan
  3

• Is “-strictMode” flag still valid?

  #51 opened 4 years ago by YyLu5
  3

• Cram references STILL not working

  #50 opened 4 years ago by agraubert
  2

• Issue with make

  #42 opened 4 years ago by joshhjang
  4

• rRNA counts differ

  #49 opened 4 years ago by kray02
  3

• Intergenic regions

  #53 opened 4 years ago by ramyar1993
  1

• Question about reading BAM file in S3 bucket

  #55 opened 4 years ago by gujjas
  9

• median TPM of gene differs from median TPM of its singleton transcript in GTEx v8

  #48 opened 4 years ago by cb4github
  2

• RNA-seQC output empty

  #46 opened 4 years ago by YyLu5
  1

• Handling of supplementary alignments

  #45 opened 4 years ago by porchard
  4

• problem with installation

  #39 opened 4 years ago by kac2053
  2

• 0 genes parsed

  #35 opened 4 years ago by jjenny
  1

• Duplicated exons issue

  #33 opened 5 years ago by AngryMaciek
  2

• STAR / Hisat2 bam not incompatible with RNA-SeQC ?

  #30 opened 5 years ago by gnilihzeux
  2

• --Unpaired option documentation

  #32 opened 5 years ago by adomingues
  3

• 5964 Segmentation fault

  #26 opened 5 years ago by ranijames
  22

• Library Complexity Estimation question

  #28 opened 5 years ago by bknisbac
  4

• Feature request: reporting Sense Rate in --unpaired mode

  #27 opened 5 years ago by bknisbac
  1

• --stranded flag reversed

  #25 opened 6 years ago by agraubert
  0