Alnus rhombifolia - Transcriptome Assembly

Summary

Name	Alnus rhombifolia - Transcriptome Assembly
Resource Type	Transcriptome Assembly
Organism	A. rhombifolia (White Alder)
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	NCBI BioProject:320832

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 Transcripts	26,186
Transcript N50	705 bp
Transcript Average Length	542 bp
Number of Proteins	14,263
Protein N50	225 aa
Protein Average Length	204 aa

Download assembled data:

	Putative Transcripts (fasta format) Alnus_rhombifolia_021816_transcripts.fasta
	Predicted ORFs (fasta format) Alnus_rhombifolia_021816_peptides.fasta

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Annotation

BLAST against the Swiss-prot protein database:

	Blastx, 1e-4 cutoff - 61% of transcripts matched a swiss-prot entry white_alder_blastx_sprot.xlsx (Excel file with best hits)
	Blastp, 1e-4 cutoff - 75% of proteins matched a swiss-prot entry white_alder_blastp_sprot.xlsx (Excel file with best hits)

BLAST against the Trembl protein database, only plant entries:

	Blastx, 1e-4 cutoff - 84% of transcripts matched a trembl entry white_alder_blastx_trembl.xlsx (Excel file with best hits)
	Blastp, 1e-4 cutoff - 94% of proteins matched a trembl entry white_alder_blastp_trembl.xlsx (Excel file with best hits)

HMMER search against Pfam database

	Excel output of all hits Alnus_rhombifolia_021816_peptides_hmmer_pfam.xlsx

SSR Pipeline

	Excel file with statistics, SSR motifs and primers (191 high quality markers) Alnus_rhombifolia_021816_transcripts.fasta.ssr_report.xlsx

Read Statistics

RNA was isolated and sequenced from pooled leaf tissues.

Illumina MiSeq Data

Library Description	Library Code	Platform	MiSeq Reads	MiSeq Bases
White Alder - pooled seedling leaf RNAs from ozone treatments (round 1, round 2)	WA1	Illumina MiSeq	1,997,227	539,065,469

Alnus rhombifolia - Transcriptome Assembly

Assembly Statistics

Annotation

Read Statistics

Illumina MiSeq Data

How to Cite