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