[maker-devel] est2genome wrong strand

[Mack, Brian]

Hi, I've noticed a what seems to be a flipping of the strand of some of my transcripts from est2genome. I assembled my directional rna-seq reads using Trinity. I've copied an example below. The blastn within maker shows the transcript aligning on the positive strand as does blastn against my genome in sequencserver. But the est2genome shows the strand to be negative. I've noticed this for quite a few transcripts while examining it in WebApollo. Any ideas what might be causing this?



Thanks,

Brian



Query= comp17103_c1_seq3 len=612 path=[8488307:0-177 8492039:178-496

>contig_69 <http://10.114.143.20:4567/get_sequence/?id=contig_69&db=/home/brian/blastdb/af70_20130423_id-modified.assembly.txt>

Length=108040



 Score =  1043 bits (1156),  Expect = 0.0

 Identities = 589/592 (99%), Gaps = 3/592 (1%)

 Strand=Plus/Plus



Query  24      TCTTTATTCTTTTATTTCCACTTGAGCAATTATTTCCGGGTCAACCTATTCGGTCGTTCT  83

               ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

Sbjct  105546  TCTTTATTCTTTTATTTCCACTTGAGCAATTATTTCCGGGTCAACCTATTCGGTCGTTCT  105605



Query  84      CTCCGTTGAGCC-TTCCCTCCCCAAGTAATATTGGAAAGTCGTTCTCTCGCTCATAATTT  142

               |||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||

Sbjct  105606  CTCCGTTGAGCCCTTCCCTCCCCAAGTAATATTGGAAAGTCGTTCTCTCGCTCATAATTT  105665




69           blastn    expressed_sequence_match         105546  106137  559        +             .               ID=69:hit:182380:3.2.0.0;Name=comp17103_c1_seq3
69           blastn    match_part         105546  106137  559        +             .               ID=69:hsp:377369:3.2.0.0;Parent=69:hit:182380:3.2.0.0;Target=comp17103_c1_seq3 24 612 +;Gap=M70 D1 M85 D1 M75 D1 M359
69           est2genome       expressed_sequence_match         105546  106137  2909      -              .               ID=69:hit:182644:3.2.0.0;Name=comp17103_c1_seq3
69           est2genome       match_part         105546  106137  2909      -              .               ID=69:hsp:377775:3.2.0.0;Parent=69:hit:182644:3.2.0.0;Target=comp17103_c1_seq3 24 612 -;Gap=M70 D1 M85 D1 M75 D1 M359
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20150320/d3f1dc4c/attachment-0002.html>