Question: Help to interpret SAM read results
0
gravatar for SmallChess
3.5 years ago by
SmallChess460
Australia
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

https://samtools.github.io/hts-specs/SAMv1.pdf

Download this pdf and study it thoroughly.

ADD REPLYlink written 3.5 years ago by Ashutosh Pandey11k
2
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 http://www.illumina.com/technology/next-generation-sequencing/paired-end-sequencing_assay.html   The read maps chr1, the mate maps another chromosome chrT

ADD COMMENTlink written 3.5 years ago by Pierre Lindenbaum114k
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