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

April 5, 2018, midnight

Category

Transcripts

Description

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

File

genome738sl.polished.consensus_isoforms_sorted.gff_.gz

Index

genome738sl.polished.consensus_isoforms_sorted.gff_.gz.tbi