Index of /EvidentialGene/arthropods/nasoniawasp/rnasm

 Name                            Last modified       Size  

 Parent Directory                25-Mar-2019 14:24      -  
 nvit1_rnaseq.assembly-info.txt  19-Aug-2011 11:58     3k  
 nvit1_rnaseq.cuff1rs13cd.gff.gz 13-Aug-2011 16:49   5.9M  
 nvit1_rnaseq.vel3rs13.gff.gz    15-Aug-2011 19:50  12.2M  
 nvit1_rnaseq.cuff1rs13cd.fa.gz  13-Aug-2011 16:56  13.9M  
 nvit1_rnaseq.vel3rs13.fa.gz     15-Aug-2011 19:31  20.6M  

Nasonia vitripennis RNA-Seq data and assemblies
2011 August, Don Gilbert, gilbertd at indiana edu

RNA-seq/EST assemblies  ================================ 

Cufflinks assemblies of Rna-seq
   14M Aug 13 16:56 nvit1_rnaseq.cuff1rs13cd.fa.gz     Transcripts
  5.9M Aug 13 16:49 nvit1_rnaseq.cuff1rs13cd.gff.gz    Locations

  cufflinks v1.0.3 ; default options

  nvit1_rnaseq.cuff1rs13cd Aug 2011, average CDS, exon spans 
    n=46261; CDS=339; Exon=893; %C/X=38  #  has 18,000 exons containing valid introns   
    n=46261; CDS=543; Exon=872; %C/X=62  # after cut out retained introns  

Velvet/Oases assemblies of Nasvit1 Rna-seq + EST paired-end and single reads 
  21M Aug 15 19:31 nvit1_rnaseq.vel3rs13.fa.gz    Transcripts
  12M Aug 15 19:50 nvit1_rnaseq.vel3rs13.gff.gz   Locations

  Rnaseq n=187,823,326; EST paired n=124,188; EST single n=51,665
    (rnaseq cleaned of rRNA align and excess duplicate mappings)
  velvet v1.1.05, oases v 0.1.22
  options: kmer=27 -min_trans_lgth=40 -ins_length_long=400 -conserveLong yes

  nvit1_rnaseq.vel3rs13 count, average CDS and exon span
    n=151038; CDS=366; Exon=679; %C/X=53  # transcript assembly mapped to genome
    n=151038; CDS=465; Exon=671; %C/X=69 # after cut retained introns

NOTE: the assemblies nvit1_rnaseq.cuff1rs13cd, nvit1_rnaseq.vel2rs13 have not been
    post-processed to cut valid introns or remove invalid UTR extensions overlapping
    reversed genes.  A further best combined assembly of these 2 and 2 other velvet
    assemblies is being produced for this.

RNA-seq Source data ===============================
  Rna-seq .fastq mapped to nasvit1asm.genome with Gsnap, version 2011-01-21 opt=-N 1 -k 14
  200 Mil mapped reads

 nvit1_s567.fq.gz        n= 7,326,584   Aug 2010  Tim Sackton
 nvit1_s009r1.fq.gz      n= 5,474,736   Oct 2010  TS
 nvit1_s3t3.fq.gz        n= 6,823,564   Oct 2010  TS
 nvit1_s016r1.fq.gz      n=   973,720   Oct 2010  TS
 
 nvit1_rs2embryo.fq.gz   n= 6,574,663   Oct 2010  XU  #  same as xu004, embryo
 036_R1.fastq.gz         n=28,415,380   June 2011 XU  VVembryo
 016_R1.fastq.gz         n=21,638,282   "         XU  VVembryo
 004_R1.fastq.gz         n=22,697,219   "         XU, VVadult, 80 bp

  642M Aug 11 21:21 VV_abdomen1.fastq.gz  n=10588790  Aug 2011 XU adult abdomen (GAIIx, 20% giraulti) 84bp
  769M Aug  4 16:18 VV_abdomen2.fastq.gz  n=xxxxxxxx  Aug 2011 XU adult abdomen (GAIIx, 20% giraulti) 40bp
  1.5G Aug  4 16:11 VV_abdomen3.fastq.gz  n=29012101  Aug 2011 XU adult abdomen (HiSeq) 51bp
  1.1G Aug 12 12:17 VV_head1.fastq.gz     n=xxxxxxxx  Aug 2011 XU adult head (GAIIx, 20% giraulti) 40bp
  1.4G Aug  4 16:21 VV_head2.fastq.gz     n=xxxxxxxx  Aug 2011 XU adult head (HiSeq) 51bp

  1.4G Aug 11 22:00 bams/nvit1_004_R1.bam
  877M Jun 10 16:38 bams/nvit1_016_R1.bam
 1020M Jun 10 16:40 bams/nvit1_036_R1.bam
  391M Jun 10 10:18 bams/nvit1_rs2embryo.bam
  283M Jun 10 17:15 bams/nvit1_s009r1.bam
   81M Jun 10 11:32 bams/nvit1_s016r1.bam
  426M Jun 10 16:37 bams/nvit1_s3t3.bam
  382M Jun 10 17:18 bams/nvit1_s567.bam
  782M Aug 11 21:49 bams/nvit1_VV_abdomen1.bam
  758M Aug 11 20:55 bams/nvit1_VV_abdomen2.bam
  1.3G Aug 12 13:18 bams/nvit1_VV_abdomen3.bam
  1.7G Aug 12 13:19 bams/nvit1_VV_head1.bam
  1.3G Aug 13 01:23 bams/nvit1_VV_head2.bam