Can you double check how the sam file is created?

shassathe / circRNA_eCLIP

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Can you double check how the sam file is created? #1

Closed byee4 closed 7 years ago

byee4 commented 7 years ago

This read: CGGGC:HWI-D00611:100:C6DB4ANXX:3:1115:12792:90810

reports a flag that is unmapped (4) but contains a contig and position:

rep1/226_igf2bp2.sai.sam

shassathe commented 7 years ago

Sometimes bwa reports an 'unreliable' or 'chimeric' alignment as 'unmapped'. I believe that is what is happening. Ignore reads such as this. I would follow whatever 'flag' was assigned.