Hi,
I noticed that tophat some times can map paired end reads to different chromosomes (see one example below). The sequences are undoubtedly of low complexity.
I haven't looked to see how often this may happen (I guess rarely), but I wanted to ask if there is an option to control this behavior in tophat?
Thanks!
HWUSI-EAS787_0001:5:31:1709:802#TTTTTT 113 chr1 23 255 81M 62678829 0 AGATCAACTAAACAGAAAATTAACAAGGAAAAAAAAACAAAACAAAACATGTATCTATAAAGCTCACTAAAGCAAAGCACA GGHEHHHE@HHHGHHHHHHHHHHHHHECGGGGGGGGHGGGGHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHDFFGGG NM:i:2
HWUSI-EAS787_0001:5:31:1709:802#TTTTTT 177 chr12 62678829 255 81M = 23 0 CTTTATAGATACATTTTTTGTTTTGTTTTTTTTTCCTTGTTAATTTTCTGTTTAGTTGATCTATCCATAAGTGTGAGTGGG #ECG@D9./9-@'7+:BCH,CCCB.CEEHHHHHDHDCG:GCE:HHHHFH5HGEB?GAAH9DHHHHHHHFHHHHHHHGHFHG NM:i:1
I noticed that tophat some times can map paired end reads to different chromosomes (see one example below). The sequences are undoubtedly of low complexity.
I haven't looked to see how often this may happen (I guess rarely), but I wanted to ask if there is an option to control this behavior in tophat?
Thanks!
HWUSI-EAS787_0001:5:31:1709:802#TTTTTT 113 chr1 23 255 81M 62678829 0 AGATCAACTAAACAGAAAATTAACAAGGAAAAAAAAACAAAACAAAACATGTATCTATAAAGCTCACTAAAGCAAAGCACA GGHEHHHE@HHHGHHHHHHHHHHHHHECGGGGGGGGHGGGGHHHHHHHHHHHHHHHHHHHHHHFHHHHHHHHHHHDFFGGG NM:i:2
HWUSI-EAS787_0001:5:31:1709:802#TTTTTT 177 chr12 62678829 255 81M = 23 0 CTTTATAGATACATTTTTTGTTTTGTTTTTTTTTCCTTGTTAATTTTCTGTTTAGTTGATCTATCCATAAGTGTGAGTGGG #ECG@D9./9-@'7+:BCH,CCCB.CEEHHHHHDHDCG:GCE:HHHHFH5HGEB?GAAH9DHHHHHHHFHHHHHHHGHFHG NM:i:1
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