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spatial overlap of predicted miRNAs
#58
JillAshey
opened
1 month ago
0
GO functional enrichment for closest genes to ncRNAs
#57
JillAshey
closed
1 month ago
1
Peve has two miRNAs assigned the same given name
#56
shedurkin
closed
2 months ago
1
Azenta RNA/sRNA-seq - QC - response needed
#55
kubu4
closed
1 month ago
7
lncRNA BLAST results and venn diagram
#54
zbengt
closed
2 months ago
14
Read length distribution for small RNAs
#53
JillAshey
closed
1 month ago
0
Annotate Proteins from three species
#52
sr320
closed
2 months ago
1
ncRNA FASTA and BED files, add summary figures to Supplemental
#51
shedurkin
opened
3 months ago
1
Change Pocillopora meandrina to Pocillopora tuahiniensis in manuscript, figures, tables
#50
JillAshey
closed
2 months ago
3
ShortStack may be incorrectly distinguishing between mature and star miRNA sequences
#49
shedurkin
opened
5 months ago
15
Rename miRNAs
#48
sr320
closed
5 months ago
3
Accidental commit/merge to main (in D-Apul)
#47
shedurkin
closed
6 months ago
1
Generate fasta file that includes short stack matches to database
#46
sr320
opened
6 months ago
4
Compare sequence similarity of mature miRNA across species and with database matches
#45
sr320
closed
5 months ago
9
Provide fasta files of miRNA from each approach
#44
sr320
closed
6 months ago
6
Visualization of ncRNA protein machinery across spcies
#43
JillAshey
closed
5 months ago
1
Writing up and finalizing methods and results
#42
JillAshey
opened
6 months ago
0
Review Javi's piRNA pipeline
#41
JillAshey
closed
2 months ago
0
Rerunning miRNA ID using merged reads
#40
shedurkin
closed
6 months ago
5
P.evermanni ShortStack problem - IndexError: list index out of range during "Screening of possible de novo microRNAs"
#39
kubu4
closed
6 months ago
29
Functional Annotation of Protein sequences
#38
sr320
closed
2 months ago
1
Add mtORF (Poc) and H2 (Por) sequences to OSF
#37
hputnam
opened
9 months ago
2
Store raw genome files to OSF account
#36
daniellembecker
closed
9 months ago
1
Add all bioinformatic workflows to the new wiki page Bioinformatic Workflows
#35
daniellembecker
opened
10 months ago
0
Add transcript fastas to wiki
#34
sr320
closed
9 months ago
12
Confirm lncRNA gtf and fasta links are correct on wiki
#33
sr320
closed
9 months ago
2
Species Identification
#32
hputnam
opened
10 months ago
2
Create OSF repo for deep dive if we do not already have one
#31
AHuffmyer
closed
10 months ago
1
Add lncRNA pipeline to repo
#30
sr320
closed
1 year ago
1
Phys + ITS2 data matrices from deep dive samples
#29
JillAshey
closed
1 year ago
3
query on P evermanii sRNA
#28
sr320
closed
1 year ago
2
Run new miRNA pipeline on evermanni data
#27
sr320
closed
2 months ago
12
add short RNA fasta and gffs to wiki
#26
sr320
closed
1 year ago
1
Add lncrna fasta and gff to wiki
#25
sr320
closed
1 year ago
0
Generate expression count matrix of lncrna, shortRNA, genes for Porites evermanni
#24
sr320
closed
1 month ago
0
Run reciprocal blast across lncRNA 3 species
#23
sr320
closed
1 month ago
0
Genome to use for Pocillopora analyses?
#22
hputnam
closed
9 months ago
2
Genome to use for P.evermanni analyses?
#21
kubu4
closed
1 year ago
4
Genome to use for A.pulchra analyses?
#20
kubu4
closed
1 year ago
2
Run short stack on DEF sRNA reads
#19
sr320
closed
1 year ago
7
Run blastn on P-ver genome using lncRNA
#18
sr320
closed
1 year ago
0
Perform hybridization analysis for lncRNA and RNAseq for A-Pver
#17
sr320
opened
1 year ago
0
Create genome feature file for IGV for A-Pver lncRNA
#16
sr320
closed
1 year ago
0
WGCNA of lncRNA and gene expression for A-Pver
#15
sr320
closed
1 year ago
0
Trimming for sRNA-seq data
#14
kubu4
closed
1 year ago
6
Add sub-efforts to deep-dive README.md for RNA/sRNAseq species
#13
kubu4
closed
1 year ago
2
Develop count matrix for short RNA data
#12
sr320
closed
1 year ago
1
Annotation gtf available for P verucosa?
#11
sr320
closed
1 year ago
3
Outline approaches for P. meandrina functional annotation and decide if update functional annotation
#10
hputnam
closed
6 months ago
3
Compare de novo transcriptome assembly to different genome gene sets.
#9
sr320
closed
1 year ago
4
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