Stats for Non-strand Specific RNA-Seq Assembly for P. adspersus

srlab@emu:~/Documents/marco/trinity_out_dir$ /home/shared/trinityrnaseq-Trinity-v2.4.0/util/TrinityStats.pl ~/Documents/owl/scaphapoda/marco/Trinity.fasta
################################
## Counts of transcripts, etc.
################################
Total trinity ‘genes’: 103033
Total trinity transcripts: 201668
Percent GC: 45.95

########################################
Stats based on ALL transcript contigs:
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Contig N10: 5975
Contig N20: 4700
Contig N30: 3922
Contig N40: 3320
Contig N50: 2792

Median contig length: 789
Average contig: 1466.72
Total assembled bases: 295789732
#####################################################
## Stats based on ONLY LONGEST ISOFORM per ‘GENE’:
#####################################################

Contig N10: 5871
Contig N20: 4550
Contig N30: 3702
Contig N40: 3023
Contig N50: 2399

Median contig length: 368
Average contig: 948.35
Total assembled bases: 97711208

Stats for Strand Specific P. adspersus RNA-Seq assembly

srlab@emu:~/Documents/marco/trinity_out_dir$ /home/shared/trinityrnaseq-Trinity-v2.4.0/util/TrinityStats.pl Trinity.fasta
################################
## Counts of transcripts, etc.
################################
Total trinity ‘genes’: 113880
Total trinity transcripts: 208395
Percent GC: 46.44

########################################
Stats based on ALL transcript contigs:
########################################

Contig N10: 5287
Contig N20: 4212
Contig N30: 3519
Contig N40: 2979
Contig N50: 2490

Median contig length: 660
Average contig: 1292.22
Total assembled bases: 269293138
#####################################################
## Stats based on ONLY LONGEST ISOFORM per ‘GENE’:
#####################################################

Contig N10: 5308
Contig N20: 4134
Contig N30: 3384
Contig N40: 2771
Contig N50: 2196

Median contig length: 361
Average contig: 892.92
Total assembled bases: 101686116

Yaamini’s Notebook: Aggregating Metaanalysis Data

I became well-aquainted NCBI SRA database today

It’s not the most user-friendly database, but it’s still pretty great! Based off of Sean and Grace’s previous searches and some of my own searches, I found C. gigas methylation data. You can read up on my methods here.

I recorded the following metadata for each run I found:

  • Project code
  • SRA study code
  • Experiment code
  • Experimental Design
  • Sample type
  • Library information (Name, Platform, Strategy, Source, Selection, Layout)
  • Run code
  • Run information (Spots, Bases, Size, GC Content)
  • Submitted by
  • Date published

All of the metadata is in this spreadsheet. Tomorrow, I’ll download the data (apparently it’s not a straightforward process).

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