laurahspencer/DuMOAR

Issues

• Re-run Salmon alignment with --gcBias flag

  #45 opened 9 months ago by laurahspencer
  6

• Annotate transcriptome

  #44 opened a year ago by laurahspencer
  11

• Re-run STAR aligner using Dungeness crab and MEGAN-scrubbed RNASeq data

  #39 opened a year ago by laurahspencer
  2

• Try mapping RNASeq R1 and R2 each alone

  #42 opened a year ago by laurahspencer
  1

• BUSCO on denovo transcriptome from MEGAN-scrubbed reads

  #41 opened a year ago by laurahspencer
  2

• Salmon to map ALL RNASeq reads to the trinity de-novo transcriptome built from MEGAN-scrubbed reads

  #43 opened a year ago by laurahspencer
  1

• MBD-BS: align and call meth status using Bismark

  #15 opened a year ago by laurahspencer
  25

• Remove bacteria sequences from RNA-seq data

  #35 opened a year ago by sr320
  3

• Get RNA quality information from sequencing facility from library prep

  #34 opened a year ago by laurahspencer
  5

• Align RNASeq to another crab genome

  #38 opened a year ago by laurahspencer
  1

• Quality trim MBD-BS data

  #8 opened a year ago by sr320
  20

• Perform functional analysis of genes containing DMLs using GenSaS annotation

  #30 opened a year ago by laurahspencer
  0

• Pull Fastas based on two annotations and assess

  #25 opened a year ago by sr320
  5

• Run Diamond blastx and Megan on crab rna-seq reads

  #26 opened a year ago by kubu4
  16

• RNASeq STAR alignment rates

  #37 opened a year ago by laurahspencer
  5

• New RNASeq approach: de-novo transcriptome from MEGAN-scrubbed reads, Salmon for counts

  #40 opened a year ago by laurahspencer
  2

• Perform DESeq2 analysis on RNASeq data

  #31 opened a year ago by laurahspencer
  3

• Assess quality of GenSAS & GAWN annotations, choose one to use in analyses

  #24 opened a year ago by laurahspencer
  15

• Submit Dungeness crab genome to GenSaS for annotation

  #3 opened a year ago by laurahspencer
  10

• Align mbdbs data to publicly available mito genome

  #27 opened a year ago by laurahspencer
  10

• Align RNASeq samples to genome using STAR for diff. expression analysis

  #32 opened a year ago by laurahspencer
  3

• Assess bacteria (non-target) sequences in MBD data

  #36 opened a year ago by sr320
  2

• Identify CT SNPs to remove from list of DMLs

  #33 opened a year ago by laurahspencer
  0

• Characterize general methylation landscape

  #28 opened 2 years ago by sr320
  0

• Determine Mitochondria Sequence in Genome

  #22 opened 2 years ago by sr320
  1

• Decide on samples to remove for MBD-BS analysis

  #17 opened 2 years ago by sr320
  11

• Decide on version of genome to use

  #23 opened 2 years ago by sr320
  24

• Submit Dungeness crab genome to NCBI

  #2 opened 2 years ago by laurahspencer
  2

• Re-run WGBS analysis using newest Dungeness genome

  #6 opened 2 years ago by laurahspencer
  3

• Quality trim RNA-seq data

  #9 opened 2 years ago by sr320
  0

• Write-up evidence/decisions regarding removing 8 samples from analysis

  #20 opened 2 years ago by laurahspencer
  0

• Write letter to NCBI from this project's "consortium" re: annotation

  #7 opened 2 years ago by laurahspencer
  4

• Ask NCBI to remove weird MBDBS-Seq samples

  #21 opened 2 years ago by laurahspencer
  0

• Run Bismark on trimmed data prior to concatenation

  #18 opened 2 years ago by sr320
  2

• Submit RNASeq and MBDBS to NCBI/SRA

  #19 opened 2 years ago by laurahspencer
  2

• Submit raw MBD-BS and RNA-Seq data to NCBI

  #13 opened 2 years ago by laurahspencer
  5

• Incorporate MiSeq data from MBDBS libraries in meth. analysis?

  #16 opened 2 years ago by laurahspencer
  2

• Add data links to Wiki

  #10 opened 2 years ago by sr320
  2

• Back up MBD-BS and RNASeq data from Sedna to Google Drive (?)

  #12 opened 2 years ago by laurahspencer
  2

• Start MBD-BS analysis

  #4 opened 2 years ago by laurahspencer
  0

• Concatenate fastq.gz files by sample (2 per sample)

  #14 opened 2 years ago by laurahspencer
  1

• Confirm two lanes per sample for MBD-BS data

  #11 opened 2 years ago by laurahspencer
  1

• Cool acronym

  #1 opened 2 years ago by laurahspencer
  3

• Pull SNPs from RNA-Seq for parentage/genetic analysis

  #5 opened 2 years ago by laurahspencer
  0