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Hi! I 've got some variable length paired-end reads as a result of adapter and quality dynamic trimming. I would like to run the latest version of tophat on this library.
1) Should I ensure that all of my reads are still paired (so that the orphaned reads whose mates were deleted because of low quality are weeded out into a separate, "singles" file)? What's the easiest tool to do this?
2) [More importantly] Which value should I set for my mate inner distance - that which is true for the longest pairs??
And on a more important note - how does tophat actually use the quality information in a read? Will it properly align a read that uniquely maps in positions 1-85 and then, due to a drop in quality, bases are miscalled at positions 86-101 (thereby increasing the number of "mismatches" artificially, if these bases were considered?)?
Thanks in advance!
1) Should I ensure that all of my reads are still paired (so that the orphaned reads whose mates were deleted because of low quality are weeded out into a separate, "singles" file)? What's the easiest tool to do this?
2) [More importantly] Which value should I set for my mate inner distance - that which is true for the longest pairs??
And on a more important note - how does tophat actually use the quality information in a read? Will it properly align a read that uniquely maps in positions 1-85 and then, due to a drop in quality, bases are miscalled at positions 86-101 (thereby increasing the number of "mismatches" artificially, if these bases were considered?)?
Thanks in advance!