Question: Help to interpret SAM read results
gravatar for SmallChess
3.5 years ago by
SmallChess460 wrote:

I have a dozen of aligned reads (against the human hg38) such as:


HISEQ:104:C5MKGANXX:7:1201:5569:32849   65      chr1    37987581        50      98M105N28M      chrT    2009424 0       GGTGCTTCCGGTGGAA....  AS:i:0  XM:i:0  XO:i:0  XG:i:0  MD:Z:126        NM:i:0  XS:A:-  NH:i:1


I don't understand why my read has a RNAME == "chr1" and RNEXT == "chrT". What does it mean? Does it mean the read maps to two different chromosomes??? My command:


tophat -p 4 -o RLC2A combined C5MKGANXX_7_RLC2A_Human_GCCAAT_R_WENCHE_STANDARD_M001_R1.fastq.gz C5MKGANXX_7_RLC2A_Human_GCCAAT_R_WENCHE_STANDARD_M001_R2.fastq.gz





tophat • 1.1k views
ADD COMMENTlink modified 3.5 years ago by Pierre Lindenbaum114k • written 3.5 years ago by SmallChess460

Download this pdf and study it thoroughly.

ADD REPLYlink written 3.5 years ago by Ashutosh Pandey11k
gravatar for Pierre Lindenbaum
3.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum114k wrote:

It's a paired-end assay   The read maps chr1, the mate maps another chromosome chrT

ADD COMMENTlink written 3.5 years ago by Pierre Lindenbaum114k
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