Hi Peng, I'll try to answer your questions in order:
-Some ESTs have polyA. Could you let me know how to tell which has polyA and which doesn't? In the track controls for the EST tracks, there is a check box labeled: "Draw a vertical green line where query has a polyA tail insertion" If you turn that on, you should be able to see which ESTs have polyA inserts. You can reach the track controls by clicking on the track name in the drop down section, or by clicking on the mini button next to the track in the display area. -Some EST are colored black and some are colored gray. What is the difference? In dense mode, the degree of darkness corresponds to the number of features aligning to the region or the degree of quality of the match. -I also see very narrow orange bands (vertical) on some ESTs. Could you please me what they mean? The narrow orange bands represent an insertion in the query sequence and they can be turned on and off in the track controls as well. There is a check box with this label: " Draw a vertical blue line for an insertion at the beginning or end of the query, orange for insertion in the middle of the query" -Why some ESTs have '>>>' or '<<<' on them, but others don't? The arrows indicate the orientation of the alignment, pointing right if the query sequence was aligned to the forward strand of the genome and left if aligned to the reverse strand. This data isn't available for all ESTs -Why some gaps are connected by single lines and some are are connected by double lines? Two lines indicate a gap in both the query and the genome, a single line indicates a gap in the query only. This track is a Pat Space Layout (PSL) track. You can read more about this type of track here: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#PSLDisplay You can read more about the coloring of alignment gaps/insertions here: http://genome.ucsc.edu/goldenPath/help/hgIndelDisplay.html I hope this has been helpful. Please feel free to ask again if you have further inquiries. Antonio Coelho UCSC Genome Bioinformatics Group Peng Yu wrote: > Some ESTs have polyA. Could you let me know how to tell which has > polyA and which doesn't? > > Some EST are colored black and some are colored gray. What is the difference? > > I also see very narrow orange bands (vertical) on some ESTs. Could you > please me what they mean? > > Why some ESTs have '>>>' or '<<<' on them, but others don't? > > Why some gaps are connected by single lines and some are are connected > by double lines? > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
