Consensus Isoseq Transcriptome from PA3 and TN19

Downloadable File
Organism: 
Heterodera glycines v2 (Soybean Cyst Nematode (v2))
Program, Pipeline Name or Method Name: 
SmartPortal, Gmap
Program, Pipeline or Method version: 
Gmap 2016-04-04
Source Name: 
H.glycines Isoseq Consensus isoforms
Time Executed: 
04/05/2018
Materials & Methods (Description and/or Program Settings): 
Samples: idx1 = W82_PA3_Eggs idx2 = W82_PA3_J2/J3 idx3 = W82_PA3_J4/Adult idx4 = W82_TN19_Eggs idx5 = W82_TN19_J4/Adult idx6 = W82_TN19_J2/J3 First reads of inserts were generated using the pacbio smrtanalysis RS_ReadsOfInsert protocol. This was done on the pool as a whole, then reads were segregated based on exact matched to the index sequences. The indexed results then each went into the isoseq protocol, which identified full length transcripts by identifying the 5' and 3' adapters as well as the polyA tail. Next the Full length nonchimeric reads are clustered for correction using the ICE algorithm that is part of the isoseq protocol. #reads were aligned with GMAP gmap -D /data013/GIF/remkv6/Baum/CamTechGenomeComparison/34_IsoSeq/ -d 738.genome -B 5 -t 16 --input-buffer-size=1000000 --output-buffer-size=1000000 -f 2 all_isoseq_reads.fasta >isoseq_738.gff
Category: