StevenWingett/FastQ-Screen

Issues

• No reference genomes were configured, please adjust configuration

  #70 opened a month ago by Linnaeus001
  4

• Reference genomes on Babraham Bioinformatics website are no longer available for download

  #69 opened 2 months ago by kuanyili
  3

• Doesn't match if U nucleotide used in sequence

  #68 opened 4 months ago by keenhl
  3

• Filtering was killed

  #65 opened 10 months ago by Eduardo-Auer
  1

• Unable to download v0.15.3 FastQ-Screen or --get_genomes

  #64 opened 10 months ago by Weng-yann
  1

• Filtering bisulfite fastq files

  #63 opened a year ago by amsparks
  3

• issue installing..

  #62 opened a year ago by chorong5155
  1

• FastQC on output

  #60 opened a year ago by christiane-morecock
  5

• Skipping DATABASE

  #61 opened a year ago by airbender97
  1

• Using pigz for parallel gzip operations

  #58 opened 2 years ago by JoshLoecker
  2

• Question- how to include no hit reads into final fastq data while screening?

  #57 opened 2 years ago by anilchauhanhp9
  1

• Only "no hits" in the output!!

  #56 opened 2 years ago by Hela06
  3

• can we download a subset of index database?

  #55 opened 2 years ago by M-gowda
  1

• Processing very long reads

  #34 opened 4 years ago by StevenWingett
  2

• --get_genomes download failed

  #47 opened 2 years ago by trfeuerborn
  8

• Fail to install GD module

  #53 opened 2 years ago by ericjuo
  1

• Support for STAR

  #52 opened 2 years ago by perinom
  2

• FastQ Screen Anaconda

  #22 opened 2 years ago by StevenWingett
  3

• Error while performing --bisulfite read mapping

  #46 opened 2 years ago by rbpisupati
  4

• v0.10.0 much slower when using higher number of threads

  #29 opened 2 years ago by sentausa
  2

• How many nucleotides (bp) need to be matched between one read of our genome and reference genome?

  #35 opened 2 years ago by lida-R
  2

• With BWA, R1 & R2 files can have very different mapping signatures

  #36 opened 2 years ago by cbird808
  7

• Changeable Bowtie2 options (--very-fast)

  #37 opened 2 years ago by LucasFVoges
  3

• Error with certificate for --get-genome

  #39 opened 3 years ago by SebastienNin
  7

• R1 and R2 generate map differently to the human genome

  #38 opened 3 years ago by simonovae
  4

• rRNA genome

  #30 opened 4 years ago by StevenWingett
  6

• How to run Fastq-screen on paired end RNA-Seq data?

  #32 opened 4 years ago by lida-R
  5

• Pairing filtered FASTQ files

  #31 opened 3 years ago by StevenWingett
  10

• Message when passed non-valid path to bowtie2

  #33 opened 4 years ago by StevenWingett
  0

• Create a DockerHub container

  #21 opened 4 years ago by StevenWingett
  4

• fastq_screen does not yield non-zero exit code when aligner returns non-zero exit code

  #28 opened 4 years ago by k1sauce
  1

• SAM or BAM files extraction after alignment

  #27 opened 4 years ago
  1

• pair-end screen

  #26 opened 4 years ago by jeongmeani
  1

• Change single MT genome to multi-species mitochondria category

  #12 opened 4 years ago by FelixKrueger
  1

• Discrepancy in ambiguous alignments between default and bisulfite mode

  #6 opened 4 years ago by FelixKrueger
  1

• FASTA files

  #20 opened 4 years ago by StevenWingett
  0

• In bisulfite mode, run Bismark using local alignments

  #11 opened 4 years ago by FelixKrueger
  1

• FastQ Screen fails to clean up after itself

  #15 opened 4 years ago by FelixKrueger
  1

• Zipping of the subset file

  #17 opened 4 years ago by StevenWingett
  1

• get_genome bisulfite combination

  #10 opened 4 years ago by StevenWingett
  1

• More info about rRNA and mitochondrial indexes

  #16 opened 4 years ago by genomics-kl
  2

• How to extract rRNA reads from metagenomic RNA-seq data

  #14 opened 4 years ago by Shicheng-Guo
  1

• more information about "vectors"?

  #13 opened 4 years ago by Shicheng-Guo
  1

• [Help/Improvment] - Filter options plus no-hits

  #9 opened 5 years ago by edsonmachado
  3

• Error when running on cluster "undefined symbol: perl_xs_handshake"

  #8 opened 5 years ago by rhondene
  2

• [Feature Request] Simplify adding genomes to config file

  #2 opened 5 years ago by FelixKrueger
  1

• Invalid bowtie path

  #4 opened 5 years ago by StevenWingett
  1

• Configuration file

  #7 opened 5 years ago by StevenWingett
  1

• [Enhancement] Add option to download bisulfite indexes

  #3 opened 5 years ago by FelixKrueger
  5

• Wrong path in config file when using --get_genomes

  #5 opened 5 years ago by tdido
  5