Summary
Name
Alnus rubra - Transcriptome Assembly
Resource Type
Transcriptome Assembly
Organism
Ontology Browser
Data Source
Source Name
: de novo assembly
Source Version
: 021816
Date Performed
Wednesday, February 17, 2016 - 20:00
Number of transcripts
29113
Average Transcript Length
496
Program, Pipeline, Workflow or Method Name
Trinity, built under bowtie-1.0.1 and samtools-0.1.19; CD-HIT-EST
Program Version
trinityrnaseq_r20131110, cd-hit-v4.6.1-2012-08-27
Cross Reference
Description and Download
Description: 
MiSeq reads from a single library were cleaned with Trimmomatic and assembled by Trinity. CD-hit with parameter -c 0.95 was used to collapse highly similar reads into a single sequence. Protein sequences were predicted using Trinity. Data has been uploaded to NCBI ( go to NCBI BioProject page).

Assembly Statistics

Number of Transcripts29,113
Transcript N50617 bp
Transcript Average Length496 bp
Number of Proteins14,657
Protein N50209 aa
Protein Average Length194 aa
Download assembled data:
Putative Transcripts (fasta format)
Predicted ORFs (fasta format)

Annotation

BLAST against the Swiss-prot protein database:
Blastx, 1e-4 cutoff - 59% of transcripts matched a swiss-prot entry
Blastp, 1e-4 cutoff - 74% of proteins matched a swiss-prot entry
BLAST against the Trembl protein database, only plant entries:
Blastx, 1e-4 cutoff - 82% of transcripts matched a trembl entry
Blastp, 1e-4 cutoff - 94% of proteins matched a trembl entry
HMMER search against Pfam database
Excel output of all hits
SSR Pipeline
Excel file with statistics, SSR motifs and primers (239 high quality markers)

Read Statistics

RNA was isolated and sequenced from pooled leaf tissues.

Illumina MiSeq Data

Library DescriptionLibrary CodePlatformMiSeq ReadsMiSeq Bases
Red Alder - pooled seedling leaf RNAs from ozone treatments (round 1, round 2)RA1Illumina MiSeq3,088,680783,469,947
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