LuyiTian/FLAMES

Issues

• FLAMES would reverse the strand

  #54 opened 2 months ago by MSQ-123
  0

• Example not working for single cell pipeline

  #53 opened 3 months ago by dominguezjorge
  0

• Facing error with minimap2 when running single cell long pipeline.py

  #52 opened 5 months ago by Aravind-sunda
  0

• versions for conda dependencies

  #49 opened 6 months ago by nick-youngblut
  2

• Compilation issue for match_cell_barcode

  #50 opened 5 months ago by maxim-h
  0

• Transcript information

  #48 opened 8 months ago by hyeon9
  0

• Gene name instead of gene_ID

  #47 opened 8 months ago by rania-o
  0

• transcript id name

  #46 opened 9 months ago by Qirongmao97
  0

• Source compilation errror

  #33 opened 2 years ago by lingminhao
  1

• bam_mutations.py

  #45 opened 10 months ago by choudharis2
  0

• error in transcript quantification step

  #44 opened a year ago by sparthib
  0

• Error during re-alignment

  #43 opened a year ago by sparthib
  1

• Compute resource allocation?

  #15 opened 3 years ago by danledinh
  2

• Run FLAMES directly from an aligned bam file.

  #42 opened a year ago by PT806
  0

• How to use multiple cores

  #41 opened a year ago by lingminhao
  0

• Missing mitochondrial transcripts in isoform_annotated.gff3

  #40 opened a year ago by koehlek99
  0

• Adapt match_cell_barcode to custom Barcode and UMI Length

  #39 opened a year ago by stambolliualen
  0

• Applying FLAMES to PacBIO

  #26 opened 2 years ago by apc1992
  0

• match_cell_barcode - output cell barcode statistics file

  #38 opened 2 years ago by maegsul
  2

• sc_long_pipeline.py--> ValueError: invalid contig `chr1`

  #37 opened 2 years ago by jeneaadams
  10

• No output from match_cell_barcode

  #36 opened 2 years ago by LI-Yan-Ming
  1

• Flanking sequence match

  #35 opened 2 years ago by lingminhao
  3

• Typo in parse_realigned_bam?

  #30 opened 2 years ago by ChangqingW
  0

• How to know how many reads are assigned to the barcode ?

  #34 opened 2 years ago by lingminhao
  0

• UMI deduplication in pipeline output?

  #32 opened 2 years ago by michael-nakai
  2

• Isoform parameters

  #29 opened 2 years ago by jchang97
  2

• FSM and FSM-match to ref

  #28 opened 2 years ago by parsboy66
  0

• empty transcript_assembly.fa file using example SIRV data

  #25 opened 2 years ago by luiseze
  1

• run match_cell_barcode, no error, no result, match_cell_barcode /data_RAGE_seq/data1 cell_barcode_stat.txt split_barcode.fastq flame_3M-february-2018.txt 2; split_barcode.fastq is zero,no other file generation。

  #12 opened 4 years ago by markme123
  7

• Config file parameters

  #23 opened 3 years ago by hacaoe
  1

• fsm_splice_comp.csv

  #22 opened 3 years ago by haowBio
  0

• Cluster annotation file

  #19 opened 3 years ago by jchang97
  3

• Using transcript_count.csv.gz matrix with popular analysis tools

  #21 opened 3 years ago by rakszewska
  1

• What's the difference

  #18 opened 3 years ago by haowBio
  1

• match_cell_barcode qnames too long

  #16 opened 3 years ago by danledinh
  2

• single cell full length RNA-seq mutation detection

  #14 opened 3 years ago by garfield-hu
  0

• minimap error using sc_long_pipeline.py

  #13 opened 4 years ago by aheravi
  1

• Demultiplexing

  #6 opened 4 years ago by callumparr
  12

• Demultiplexing issues

  #10 opened 4 years ago by yangao07
  3

• where is your whiltelist

  #11 opened 4 years ago by markme123
  1

• GTF format error?

  #9 opened 4 years ago by danledinh
  1

• FLAMES vs FLAIR

  #8 opened 4 years ago by danledinh
  1

• config file

  #7 opened 4 years ago by aheravi
  3