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I just don't get it, do I need to remove these reads from my .bam file?
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They are "unexpected". One part of the read goes to one region of the genome, the other part of the read goes to another (not nearby) part of the genome, possibly another chromsome.
Though in this terminology it also means "fusion genes".
They are interesting in Cancer studies (and other studies).
What exactly are you doing?
Typically, you don't need to remove them. -
I made another post about an issue that I had with supplementary alignments.
I mapped my reads using bwa, then I filtered out the .bam file so I could obtain the unmapped reads.
Then I tried to convert the .bam file to 2 paired end .fq files, but I got this warning:
*****WARNING: Query M00532:8:000000000-A17VF:1:2114:24702:5749 is marked as paired, but it's mate does not occur next to it in your BAM file. Skipping.
The SAM flag for all these reads is 2121 and it appears such as this:
M00532:8:000000000-A17VF:1:2114:24702:5749 73 NODE_321_length_580971_cov_15.123657 246952 60 88S167M = 246952 0 CCTGTTCGTCGTTGCCCCCCCCCACCCCCCCCCCCTCCCCCCCCCACCCCCCCCCCCCCCCCCCACCGCCCACCCCCCCCCCCCCCCAGGCGCGGTTATCCAGCATTTTCACGTTCAGCTTCAGCTGGCTCAGTTGATCCACCAGCTGTTGATCGGCCATGGCGCTACCCATAACGCCCAAGAATCCACACGCTGCCGTCAAAGCGGCAAGCGCGCTCAGTTTGAATGCGTTCATCTTCTCATCCTTCCTAATTA ,5,,557555555555866655C555CCHH55C44)444=B1222'.0A...5....8<D.'..'.0)..
08ADDDD......'.'.......).00?CE?EE?AEEEEEE8?EEEEEEEC::CE?A?CECC?CEEEEEEEECC*0*:?::?AEDE?CA?CDE2'.AEEC?*0)...00.00*0:*0*0'.)).0...0)*0*0'.2;8888'4')8:***0*0***)08):******00*******00:??* NM:i:8 MD:Z:78C6C13C0A0T2T9G45T6 AS:i:127 XS:i:19 RG:Z:cof1 SA:Z:NODE_281_length_33_cov_9.606061,2,+,14S50M191S,18,2;
M00532:8:000000000-A17VF:1:2114:24702:5749 2121 NODE_281_length_33_cov_9.606061 2 18 14H50M191H = 2 0 CCCCCCCCCACCCCCCCCCCCTCCCCCCCCCACCCCCCCCCCCCCCCCCC 55866655C555CCHH55C44)444=B1222'.0A...5....8<D.'.. NM:i:2 MD:Z:9C11C28 AS:i:40 XS:i:33 RG:Z:cof1 SA:Z:NODE_321_length_580971_cov_15.123657,246952,+,88S167M,60,8; XA:Z:NODE_281_length_33_cov_9.606061,+1,39S48M168S,3;NODE_281_length_33_cov_9.606061,+24,14S42M199S,2;
M00532:8:000000000-A17VF:1:2114:24702:5749 133 NODE_321_length_580971_cov_15.123657 246952 0 * = 246952 0 GCCTGTGCGCAACCCGCCGCGCCGCCGCCCTCCCCCCCCTTTTCTCCTTCTTCCCCCCCCTTCCTCCCCTCCTCCCCCCCTCCTCCTCCTCCCCCCCTCCCCTTCCTTTCGGTGCTGAACGTGCTGAAACAAGTAAATTTTATCTTCAAGACTACTGATTTGAATACTATTCATGACCCGGAATATAAGCACTGCATTATGCCTATTTTCAGACATTCTCAAAATACAGTGATCACCCACACAGTTCTCCTCTCC ,,,,,<-<@7@@@@@@6+655++555+555*5C+>CCCC);++4+4=++224@2;9
28:008;@E99(66(;;((.''-(//66.(.//(-('..'(//96-6((/..('/('((/(/((--((./((<((/(/(////(/(/(/(./(/((//((///(((/((/(/(/(/((//6''''(/(((.(/;((/6((/66((/(////((((/(//((/((((/(/(((((((/(((((-(((/(/(./(/((( AS:i:0 XS:i:0 RG:Z:cof1
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2121 is not a valid flag. Odd.Comment
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My mistake; the last flag bit, "supplementary alignment", is new. Time to download a new version of the sam format specification
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bump still need helpComment
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