Hi, someone knows what is the sequence on top of IGB sequence windows? I think it's a sort of consensus sequence but I don't understand why some SNP are showed and some are not.
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netsam •
Hello netsam,
My name is Mason Meyer, IGB Support Specialist. Thanks for taking the time to post your IGB question on Biostars. I understand you are wondering why there is a darker row of models that appear at the top of the data track, is this correct? I am happy to help answer this question!
The row at the top you are referring to is the Summary Row. This row indicates there is some number of reads that are not being shown. To see them, you can adjust the stack height by right-clicking a track label and choosing Set Stack Height to manually set the height or Optimize Stack Height to automatically show all the reads. Here is a link to a page in our user's guide that explains how to adjust the stack height in more detail: https://wiki.transvar.org/display/igbman/Visualizing+read+alignments#Visualizingreadalignments-Adjuststackheight
I hope this comment answers your questions completely. If you have anymore follow-up questions on this or another IGB topic, please don't hesitate to let us know. If you would like, you can also contact us directly by referring to the Get Help page on our website. Thanks again, netsam!
Thanks, I really appreciated your help. Now, after I have optimized the stack height I can see all the reads aligned to my reference genome (MtDNA of Gray wolf), but I no longer see any polymorphism (SNP). I see it only if I click on minus button like in figure. I have to study D-LOOP region of MtDNA in different samples.
Hello again netsam,
You can actually create a coverage graph track by right-clicking your track label of interest and selecting Track Operations > Depth Graph (All). Here is a page in our user's guide that discusses "Depth Graphs": https://wiki.transvar.org/display/igbman/Creating+graph+tracks+from+annotations+tracks#Creatinggraphtracksfromannotationstracks-DepthGraph(All)
I hope this helps answer your question and allows you to produce your visualization of interest. If you have any additional questions, please let me know. Thanks again netsam!
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