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DuMOAR
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Re-run Salmon alignment with --gcBias flag
#45
laurahspencer
closed
4 months ago
3
Annotate transcriptome
#44
laurahspencer
opened
8 months ago
11
Salmon to map ALL RNASeq reads to the trinity de-novo transcriptome built from MEGAN-scrubbed reads
#43
laurahspencer
closed
8 months ago
1
Try mapping RNASeq R1 and R2 each alone
#42
laurahspencer
closed
8 months ago
1
BUSCO on denovo transcriptome from MEGAN-scrubbed reads
#41
laurahspencer
closed
8 months ago
2
New RNASeq approach: de-novo transcriptome from MEGAN-scrubbed reads, Salmon for counts
#40
laurahspencer
closed
9 months ago
2
Re-run STAR aligner using Dungeness crab and MEGAN-scrubbed RNASeq data
#39
laurahspencer
closed
8 months ago
2
Align RNASeq to another crab genome
#38
laurahspencer
closed
8 months ago
1
RNASeq STAR alignment rates
#37
laurahspencer
closed
9 months ago
5
Assess bacteria (non-target) sequences in MBD data
#36
sr320
opened
1 year ago
2
Remove bacteria sequences from RNA-seq data
#35
sr320
closed
8 months ago
3
Get RNA quality information from sequencing facility from library prep
#34
laurahspencer
closed
8 months ago
5
Identify CT SNPs to remove from list of DMLs
#33
laurahspencer
opened
1 year ago
0
Align RNASeq samples to genome using STAR for diff. expression analysis
#32
laurahspencer
closed
11 months ago
3
Perform DESeq2 analysis on RNASeq data
#31
laurahspencer
opened
1 year ago
3
Perform functional analysis of genes containing DMLs using GenSaS annotation
#30
laurahspencer
opened
1 year ago
0
Characterize general methylation landscape
#28
sr320
opened
1 year ago
0
Align mbdbs data to publicly available mito genome
#27
laurahspencer
closed
11 months ago
10
Run Diamond blastx and Megan on crab rna-seq reads
#26
kubu4
closed
9 months ago
16
Pull Fastas based on two annotations and assess
#25
sr320
closed
9 months ago
5
Assess quality of GenSAS & GAWN annotations, choose one to use in analyses
#24
laurahspencer
closed
11 months ago
15
Decide on version of genome to use
#23
sr320
closed
1 year ago
24
Determine Mitochondria Sequence in Genome
#22
sr320
closed
1 year ago
1
Ask NCBI to remove weird MBDBS-Seq samples
#21
laurahspencer
opened
1 year ago
0
Write-up evidence/decisions regarding removing 8 samples from analysis
#20
laurahspencer
opened
1 year ago
0
Submit RNASeq and MBDBS to NCBI/SRA
#19
laurahspencer
closed
1 year ago
2
Run Bismark on trimmed data prior to concatenation
#18
sr320
closed
1 year ago
2
Decide on samples to remove for MBD-BS analysis
#17
sr320
closed
1 year ago
11
Incorporate MiSeq data from MBDBS libraries in meth. analysis?
#16
laurahspencer
closed
1 year ago
2
MBD-BS: align and call meth status using Bismark
#15
laurahspencer
closed
8 months ago
25
Concatenate fastq.gz files by sample (2 per sample)
#14
laurahspencer
closed
1 year ago
1
Submit raw MBD-BS and RNA-Seq data to NCBI
#13
laurahspencer
closed
1 year ago
5
Back up MBD-BS and RNASeq data from Sedna to Google Drive (?)
#12
laurahspencer
opened
1 year ago
2
Confirm two lanes per sample for MBD-BS data
#11
laurahspencer
opened
1 year ago
1
Add data links to Wiki
#10
sr320
opened
1 year ago
2
Quality trim RNA-seq data
#9
sr320
closed
1 year ago
0
Quality trim MBD-BS data
#8
sr320
closed
8 months ago
20
Write letter to NCBI from this project's "consortium" re: annotation
#7
laurahspencer
opened
1 year ago
4
Re-run WGBS analysis using newest Dungeness genome
#6
laurahspencer
opened
1 year ago
3
Pull SNPs from RNA-Seq for parentage/genetic analysis
#5
laurahspencer
opened
1 year ago
0
Start MBD-BS analysis
#4
laurahspencer
closed
1 year ago
0
Submit Dungeness crab genome to GenSaS for annotation
#3
laurahspencer
closed
11 months ago
10
Submit Dungeness crab genome to NCBI
#2
laurahspencer
closed
1 year ago
2
Cool acronym
#1
laurahspencer
closed
1 year ago
3