Summary
Name
Alnus rhombifolia - Transcriptome Assembly
Resource Type
Transcriptome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Alnus rhombifolia
Data Source
Source Name
: de novo assembly
Source Version
: 021816
Date Performed
Wednesday, February 17, 2016 - 20:00
Number of transcripts
26186
Average Transcript Length
542
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 Transcripts26,186
Transcript N50705 bp
Transcript Average Length542 bp
Number of Proteins14,263
Protein N50225 aa
Protein Average Length204 aa
Download assembled data:
Putative Transcripts (fasta format)
Predicted ORFs (fasta format)
  • Download
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Annotation

BLAST against the Swiss-prot protein database:
Blastx, 1e-4 cutoff - 61% of transcripts matched a swiss-prot entry
Blastp, 1e-4 cutoff - 75% of proteins matched a swiss-prot entry
BLAST against the Trembl protein database, only plant entries:
Blastx, 1e-4 cutoff - 84% 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 (191 high quality markers)

Read Statistics

RNA was isolated and sequenced from pooled leaf tissues.

Illumina MiSeq Data

Library DescriptionLibrary CodePlatformMiSeq ReadsMiSeq Bases
White Alder - pooled seedling leaf RNAs from ozone treatments (round 1, round 2)WA1Illumina MiSeq1,997,227539,065,469
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