The flag. It is the mate-unmap bit that can be mislabeled. The unmap bit is always set correctly.
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Originally posted by lh3 View PostThe flag. It is the mate-unmap bit that can be mislabeled. The unmap bit is always set correctly.
And sometimes, the first best hit appear in in "XA" again, but sometimes not, why? What's the difference between the first best hit and best hits in "XA"?
An example is as follows, where the "hg19_refGene_NM_001190241" appear in "XA" again:
GA-C_0001:1:1:1519:3751#0 83 hg19_refGene_NM_001190241 2021 0 49M = 1932 -138 NCTTTCTCATAAGAATGAAATCTTGGAAATTGCTCTGGATCAAAAAGGA BB
BBBbb_bb_abbbabbb`bbbbbaabbbbb`bbbbbbbabbabbbbb XT:A:R NM:i:1 SM:i:0 AM:i:0 X0:i:3 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T48 XA:Z:hg19_refGene_NM_020800,-1801,49M,1;hg
19_refGene_NM_001190241,-2021,49M,1;
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Originally posted by edge View PostHi Yuan,
Do you mind to explain what is the exact meaning of 0, 4, 16 if I map my single-end read against reference transcript by using bowtie?
As I know, 4 is refer to unmapped.
How about 0 and 16 represent?
Thanks.
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Hi Edge,
This page is probably useful for you: http://picard.sourceforge.net/explain-flags.html
20 means the read mapped in reverse strand and also the read is unmapped.
I know it's confusing. But the read is considered unmapped because it mapped to two different contigs (i.e. end of one contig and the start of another contig). You can check the read with the flag 20. It should be few bases from the end of the contig.
Thanks.
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