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<pre>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? <o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Thanks,<o:p></o:p></pre>
<pre>Brian<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><b>Query= comp17103_c1_seq3 len=612 path=[8488307:0-177 8492039:178-496<o:p></o:p></b></pre>
<pre>><a href="http://10.114.143.20:4567/get_sequence/?id=contig_69&db=/home/brian/blastdb/af70_20130423_id-modified.assembly.txt" target="_blank">contig_69 </a><a name="contig_69"></a> <o:p></o:p></pre>
<pre>Length=108040<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre> Score = 1043 bits (1156), Expect = 0.0<o:p></o:p></pre>
<pre> Identities = 589/592 (99%), Gaps = 3/592 (1%)<o:p></o:p></pre>
<pre> Strand=Plus/Plus<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Query 24 TCTTTATTCTTTTATTTCCACTTGAGCAATTATTTCCGGGTCAACCTATTCGGTCGTTCT 83<o:p></o:p></pre>
<pre> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||<o:p></o:p></pre>
<pre>Sbjct 105546 TCTTTATTCTTTTATTTCCACTTGAGCAATTATTTCCGGGTCAACCTATTCGGTCGTTCT 105605<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Query 84 CTCCGTTGAGCC-TTCCCTCCCCAAGTAATATTGGAAAGTCGTTCTCTCGCTCATAATTT 142<o:p></o:p></pre>
<pre> |||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||<o:p></o:p></pre>
<pre>Sbjct 105606 CTCCGTTGAGCCCTTCCCTCCCCAAGTAATATTGGAAAGTCGTTCTCTCGCTCATAATTT 105665<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">69 blastn expressed_sequence_match 105546 106137 559 + . ID=69:hit:182380:3.2.0.0;Name=comp17103_c1_seq3<o:p></o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
<p class="MsoNormal">69 est2genome expressed_sequence_match 105546 106137 2909 - . ID=69:hit:182644:3.2.0.0;Name=comp17103_c1_seq3<o:p></o:p></p>
<p class="MsoNormal">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<o:p></o:p></p>
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