Comments (2)
For the time being, it is recommended to separate chimeric reads and concordant reads for STAR. For chimeric split-read alignments, there are multiple SAM records corresponding to one paired-end read, however only one record is marked as chimeric. This may lead to erroneous or missing edges in SQUID's segment graph when the records are mixed with all other concordant SAM records, and finally reduces the accuracy. So when you are STAR available, it is recommended to NOT use WithinBam option.
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ok, thanks!
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