Help to interpret SAM read results

Question

[scchess]

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

[Ashutosh Pandey]

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

Download this pdf and study it thoroughly.

Answer 1

[Pierre Lindenbaum]

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