<div dir="ltr">Hi,<div> I just installed miso using '<span style="color:rgb(64,64,64);font-family:Consolas,'Andale Mono WT','Andale Mono','Lucida Console','Lucida Sans Typewriter','DejaVu Sans Mono','Bitstream Vera Sans Mono','Liberation Mono','Nimbus Mono L',Monaco,'Courier New',Courier,monospace;font-size:12px;line-height:1.5">pip install misopy' on Mac. But when I type miso I got the following error:</span></div><div><span style="color:rgb(64,64,64);font-family:Consolas,'Andale Mono WT','Andale Mono','Lucida Console','Lucida Sans Typewriter','DejaVu Sans Mono','Bitstream Vera Sans Mono','Liberation Mono','Nimbus Mono L',Monaco,'Courier New',Courier,monospace;font-size:12px;line-height:1.5">-------------------------</span></div><div><span style="color:rgb(64,64,64);font-family:Consolas,'Andale Mono WT','Andale Mono','Lucida Console','Lucida Sans Typewriter','DejaVu Sans Mono','Bitstream Vera Sans Mono','Liberation Mono','Nimbus Mono L',Monaco,'Courier New',Courier,monospace;font-size:12px;line-height:1.5">$miso</span></div><div>
<p class=""><span class="">MISO (Mixture of Isoforms model)</span></p>
<p class=""><span class="">Probabilistic analysis of RNA-Seq data for detecting differential isoforms</span></p>
<p class=""><span class="">Use --help argument to view options.</span></p>
<p class=""><span class=""></span><br></p>
<p class=""><span class="">Using MISO settings file: /usr/local/lib/python2.7/site-packages/misopy/settings/miso_settings.txt</span></p>
<p class=""><span class="">Error: Settings file /usr/local/lib/python2.7/site-packages/misopy/settings/miso_settings.txt does not exist.</span></p><p class=""><span class="">-------------------------------------</span></p><p class=""><span class=""><br></span></p><p class=""><span class="">I also tried index_gff as below and finally </span>Loaded 0 genes:</p>
<p class=""> $ index_gff --index ref_annotation1.gff indexed/<br></p>
<p class=""><span class="">Indexing GFF...</span></p>
<p class=""><span class=""> - GFF: /Users/shucheng/Documents/IGV/ref_annotation1.gff</span></p>
<p class=""><span class=""> - Outputting to: /Users/shucheng/Documents/IGV/indexed</span></p>
<p class=""><span class="">WARNING: No entries found for gene US7 in GFF /Users/Dawn/Documents/IGV/ref_annotation1.gff</span></p>
<p class=""><span class="">Skipping gene US7...</span></p><p class="">------------------------</p><p class="">Is there any help?</p><p class="">Thanks!</p><p class="">Dawn</p>
<p class=""><br></p></div></div>