Chimeric.out.junction File
If there are chimeric alignments present in the sample, then a supplementary Chimeric.out.junction file is also output. This file contains information about split-reads that can be used to perform downstream gene fusion detection. Each line contains one chimerically aligned read. The columns of the file are as follows:
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1.
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Chromosome of the donor. |
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2.
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First base of the intron of the donor (1-based). |
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4.
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Chromosome of the acceptor. |
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5.
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First base of the intron of the acceptor (1-based). |
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6.
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Strand of the acceptor. |
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7.
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N/A—not used, but is present to be compatible with other tools. It will always be 1. |
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8.
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N/A—not used, but is present to be compatible with other tools. It will always be *. |
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9.
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N/A—not used, but is present to be compatible with other tools. It will always be *. |
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11.
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First base of the first segment, on the + strand. |
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12.
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CIGAR of the first segment. |
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13.
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First base of the second segment. |
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14.
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CIGAR of the second segment. |
CIGARs in this file follow the standard CIGAR operations as found in the SAM specification, with the addition of a gap length L that is encoded with the operation p. For paired end reads, the sequence of the second mate is always reverse complemented before determining strandedness.
The following is an example entry that shows two chimerically aligned read pairs, in which one of the mates is split, mapping segments of chr19 to chr12. Also shown are the corresponding SAM records associated with these entries.
chr19 580462 + chr12 120876182 + 1 * * R_15448 571532 49M8799N26M8p49M26S 120876183 49H26M
chr19 580462 + chr12 120876182 + 1 * * R_15459 571552 29M8799N46M8p29M46S 120876183 29H46M
R_15448:1 99 chr19 571531 60 49M8799N26M = 580413
R_15448:2 147 chr19 580413 60 49M26S = 571531
R_15448:2 2193 chr12 120876182 15 49H26M chr19 571531
R_15459:1 99 chr19 571551 60 29M8799N46M = 580433
R_15459:2 147 chr19 580433 4 29M46S = 571551
R_15459:2 2193 chr12 120876182 15 29H46M chr19 571551
