Help to interpret SAM read results
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
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1 answer
It's a paired-end assay http://www.illumina.com/technology/next-generation-sequencing/paired-end-sequencing_assay.html The read maps to chr1, the mate maps to another chromosome chrT
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https://samtools.github.io/hts-specs/SAMv1.pdf
Download this pdf and study it thoroughly.