How can I dissect .sam files in text editor??

[JacquesT]

Hello everyone!

I'm new to bioinformatics.
I have some questions about reading (eye-balling) a .sam file.

For example:

@SQ SN:HPV11REF LN:7931
@SQ SN:HPV16REF LN:7846
@SQ SN:HPV18REF LN:7857
@SQ SN:HPV31REF LN:7906
@SQ SN:HPV33REF LN:7909
@SQ SN:HPV35REF LN:7879
@SQ SN:HPV39REF LN:7833
@SQ SN:HPV45REF LN:7858
@SQ SN:HPV51REF LN:7808
@SQ SN:HPV52REF LN:7942
@SQ SN:HPV56REF LN:7845
@SQ SN:HPV58REF LN:7824
@SQ SN:HPV59REF LN:7896
@SQ SN:HPV6REF LN:7996
@SQ SN:HPV1REF LN:7816
@SQ SN:HPV2REF LN:7860
@SQ SN:HPV3REF LN:7820
@SQ SN:HPV4REF LN:7353
@SQ SN:HPV5REF LN:7746
@SQ SN:HPV7REF LN:8027
@SQ SN:HPV8REF LN:7654
@SQ SN:HPV9REF LN:7434
@SQ SN:HPV10REF LN:7919
@SQ SN:HPV34REF LN:7723
@SQ SN:HPV40REF LN:7909
@SQ SN:HPV42REF LN:7917
@SQ SN:HPV43REF LN:7975
@SQ SN:HPV44REF LN:7833
@SQ SN:HPV53REF LN:7859
@SQ SN:HPV54REF LN:7759
@SQ SN:HPV61REF LN:7989
@SQ SN:HPV68REF LN:7822
@SQ SN:HPV69REF LN:7700
@SQ SN:HPV70REF LN:7905
@SQ SN:HPV72REF LN:7989
@SQ SN:HPV73REF LN:7700
@SQ SN:HPV80REF LN:7427


{BWA instruction}


MSQ-M1307R:269:000000000-D24BN:1:1101:15163:1383 (QNAME)
99 (FLAG)
HPV56REF (RNAME)
6262 (Position of the leftmost base)
60 (Mapping quality, Phred)
151M (CIGAR)
= (Mate Reference sequence NaMe (`=' if same as RNAME) )
6268 (1-based Mate POSition)
157 ( inferred Template LENgth (insert size))

ACATTGTACAATCCACCTGTAAATATCCTGACTATTTAAAAATGTCTGCAGATGCCTATGGTGATTCTATGTGGTTTTACTTACGCAGGGAACAATTATTTGCCAGACATTATTTTAATAGGGCTGGTAAAGTTGGGGAAACAATACCTGC

BCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHGHGHHHHHHGGGGGGGHGHHHHHHHHHHHHGHGHHHHHHHHHHHHHHHHHGGFHGHHHHHHGGGGHHHHHHHHHHH

NM:i:0 (OPTional fields in the format “ TAG:VTYPE:VALUE”)

MD:Z:151

AS:i:151

XS:i:0


In this first read of the sam file, I pressed "Enter" when seeing a "Tabulation", for better understanding each part.

Now, my question is about the following (copied) line (that you can find above):
= (Mate Reference sequence NaMe (`=' if same as RNAME) )

Does this mean: "if it were not '=' but 'gene X', then 'gene X' is contiguous to 'HPV56REF'(RNAME)." ???

Thank you so much for your precious help!!

Jacques T

[GenoMax]

Have you checked out SAM format specification?

[JacquesT]

Thanks GenoMax!!!

No I didn't look at that .pdf

Still, tell me if I am wrong:
In "Ref. name of the mate/next read": "next read", does it mean the one encompassing 2 genes if RNAME is not "="?

[mastal]

Mate Reference Sequence will not be '=' if the mate maps to a different contig or chromosome (the sequences listed with @SQ at the start of the sam file).

Occasionally you get read pairs where the 2 reads of the pair map to different chromosomes.

[JacquesT]

OK. It's clearer now. Thanks Mastal

Just in case I didn't understand, I have a dumb question: each read and its mate read are from the same sequence, except that one is forward and the other is reverse. Right?

[mastal]

Yes, each read and its mate are from the same fragment, starting from different ends of the fragment.