deweylab/RSEM

Issues

• RSEM issue with 1 sample: The adjacent two lines do not represent the two mates of a paired-end read!

  #222 opened 2 months ago by sarahweitzman
  0

• fatal error: buffer size for SJ output is too small Solution: increase input parameter --limitOutSJcollapsed

  #218 opened 3 months ago by sopenaml
  3

• Different read counts from STAR and RSEM

  #221 opened 3 months ago by gohweixun
  1

• rsem-extract-reference-transcripts fails with "Error Message: Strand is neither '+' nor '-'!"

  #220 opened 3 months ago by J-Moravec
  0

• Single-end fragment length mean and SD

  #219 opened 4 months ago by byqmed
  0

• Not sure if rsem is using --num-threads option...

  #217 opened 5 months ago by siyer-broad
  0

• rsem-generate-ngvector command not found

  #215 opened 7 months ago by yma122
  1

• Two mates are aligned to two different transcripts

  #214 opened 6 months ago by albustruong
  1

• The SAM/BAM file declares less than one reference sequence!

  #201 opened a year ago by Heterosigma
  2

• bam only containing aligned reads produced different expression profile

  #216 opened 6 months ago by TwoFlowers1
  0

• cleaned.fq.gz: command not found

  #213 opened 7 months ago by albustruong
  3

• Gtf file

  #212 opened 8 months ago by luisafmc
  0

• rsem-parse-alignments and rsem-build-read-index

  #211 opened 8 months ago by project-FSL
  0

• RSEM deal with multimapping?

  #206 opened 9 months ago by marwa38
  1

• make install error

  #187 opened 2 years ago by shun1w
  1

• Using STAR BAMs from genomic alignment

  #210 opened 9 months ago by charlesdavid
  2

• rsem-prepare-reference arguments

  #209 opened 9 months ago by baizhantianyu
  0

• error when using convert-sam-for-rsem to a RSEM compatible BAM file.

  #208 opened 9 months ago by qxf1995
  0

• Pearl error

  #207 opened 10 months ago by ericabrophy
  0

• about gffcompare

  #205 opened a year ago by fafuyyk
  0

• Problem implementing a reverse-strand specific analysis

  #204 opened a year ago by sknaack
  2

• genomeSAsparseD option for RSEM Star?

  #202 opened a year ago by Leelab-623
  0

• single-cell-prior is not giving me any values

  #196 opened 2 years ago by TdzBAS
  1

• how to simulate single-end reads?

  #200 opened a year ago by yhg926
  0

• import using tximport for the rsem count table to get integers?

  #199 opened a year ago by marwa38
  0

• gene id

  #198 opened 2 years ago by km-2021
  0

• rsem-calculate-expression

  #197 opened 2 years ago by km-2021
  0

• Does RSEM need HI:i:<n> tag to correctly process multimappers?

  #191 opened 2 years ago by apredeus
  2

• to run RSEM for 3 samples

  #195 opened 2 years ago by anitha-2211
  1

• make install error

  #185 opened 3 years ago by eidamama
  2

• No valid read to estimate the length distribution!

  #194 opened 2 years ago by TdzBAS
  1

• rsem-prepare-reference with filtered GTF

  #193 opened 2 years ago by TdzBAS
  0

• differential splicing simulation

  #192 opened 2 years ago by TdzBAS
  0

• Does STAR index need to be generated with the FASTA outputted by rsem-prepare-reference or can I use the same genome file provided to rsem-prepare-reference?

  #179 opened 3 years ago by etrh
  12

• Inconsistent results in rsem-plot-model

  #190 opened 2 years ago by sschrstn
  0

• "make" error on mac (log attached)

  #189 opened 2 years ago by thisisamirv
  1

• positive counts with ZERO effective length, FPKM and TPM

  #188 opened 2 years ago by gianfilippo
  0

• How can I get the gene expression only with uniquely mapped reads by rsem-calculate-expression?

  #186 opened 2 years ago by zjuzexian
  0

• RSEM can not recognize reference sequence name

  #184 opened 3 years ago by brianpenghe
  1

• expression level of some genes is different when watching BAM file

  #183 opened 3 years ago by dahun73
  2

• rsem-calculate-expression working just with sudo in front

  #182 opened 3 years ago by mavino
  1

• Is it necessary to provide a BAI file to RSEM Calculate Expression when `--alignments` mode is used?

  #180 opened 3 years ago by etrh
  1

• About samtools

  #178 opened 3 years ago by luisafmc
  0

• rsem-generate-data-matrix error

  #177 opened 3 years ago by yukoyoshida
  0

• Link to website give 403

  #176 opened 3 years ago by nh13
  1

• use pre-built STAR indices

  #175 opened 3 years ago by AtheerAS
  3

• rsem-tbam2gbam soft-clipping (and other) errors

  #174 opened 3 years ago by joegeorgeson
  0

• prepare reference

  #172 opened 3 years ago by BaylieRW
  1

• The issue about make

  #173 opened 3 years ago by wbc569668815
  0

• Issue with rsem-prepare-reference!

  #170 opened 3 years ago by g-s-2018
  0