Samtools Tview Iupac

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11.8 years ago

sunhanice ▴ 240

I wonder why there are K in the first line. It seems that the K doesnt mean G/T here, because only one read mapped in the position, and there are not mismatch in this read.

Could anyone help me? thanks

enter image description here

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ADD COMMENT • link 11.8 years ago by sunhanice ▴ 240

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Can you show us the SAM record of that read please.

ADD REPLY • link 11.8 years ago by Pierre Lindenbaum 164k

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the read in the sam file is :

SRR040290.11836137 0 chr2 10263590 255 48M * 0 0 CCATCGAGTACCATGATATCTGGCAGATGTATAAGAAGGCAGAGGCTT WQPX_][\VRY[SKOM;=KMOGCDJO29PQ:!!4NB605DJG8+!!!! XA:i:1 MD:Z:48 NM:i:0 CM:i:8

ADD REPLY • link 11.8 years ago by sunhanice ▴ 240

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but this raw read in the fastq file is T20013232213101312333221031222113222220203122202023, if I convert it to atcg, I can get CCCATCGAGTACCATGATATCTGGCAGAGTGCTCTCTTCCGTCTCCTTCG, it seems that the only first part of this read(CCCATCGAGTACCATGATATCTGGCAGA) is the same as the reference, is it soft clipped mapped?

ADD REPLY • link 11.8 years ago by sunhanice ▴ 240

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