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  • Bioscope sam output

    Does anyone know if Bioscope sam output's mapping quality score follows sam specifications? I noticed I have a lot of 0's in the 4th mapping quality column in my Bioscope output alignments. I also see some 100's. I thought mapping quality is 0-99?
    Last edited by damiankao; 03-22-2010, 07:17 AM.

  • #2
    Originally posted by damiankao View Post
    Does anyone know if Bioscope sam output's mapping quality score follows sam specifications? I noticed I have a lot of 0's in the 4th mapping quality column in my Bioscope output alignments. I also see some 100's. I thought mapping quality is 0-99?
    Mapping quality is between 0 and 255.

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    • #3
      Originally posted by damiankao View Post
      Does anyone know if Bioscope sam output's mapping quality score follows sam specifications? I noticed I have a lot of 0's in the 4th mapping quality column in my Bioscope output alignments. I also see some 100's. I thought mapping quality is 0-99?
      what version of BS are you using? Those that version dumps BAMs directly or you have to postprocess to convert to BAM/SAM?

      Can you dump some entries from your BAM?
      -drd

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      • #4
        I am using the version that dumps .bam. Then I post-process to .sam and cleaned it up for cufflinks.

        Here's a few entries with really low scores.
        Code:
        1847_606_2027	256	Contig78899	2917	0	31M19H	*	0	0	TGAATGACCTTGACCTACTTTTCAATGACCT	DIFE>DIII'&->E4AIHFH;.:IIFAFID2	XS:A:+
        763_1093_180	256	Contig78899	2917	1	34M16H	*	0	0	TGAATGACCTTGACCTACTTTTCAATGACCTTGA	IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII:H	XS:A:+
        955_1354_927	256	Contig78899	2917	1	27M23H	*	0	0	TGAATGACCTTGACCTACTTTTCAATG	77CIEEIIIIHFDIIIHGIIIDIIIA1	XS:A:+
        1347_1328_414	256	Contig78899	2919	0	15H31M4H	*	0	0	AATGACCTTGACCTACTTTTCAATGACCTTG	EAIIIIE<0:%%II>FIIIIIIIIIIIIDII	XS:A:+
        1062_1345_1564	272	Contig78899	2919	0	21H29M	*	0	0	AATGACCTTGACCTACTTTTCAATGACCT	I6EIII&&IIIGIIIII=>I>%%:IIICI	XS:A:-
        1648_875_1465	272	Contig78899	2921	0	22H28M	*	0	0	TGACCTTGACCTACTTTTCAATGACCTT	"7G7*-;FE<1AI=4##IIIIIIIIIII	XS:A:-
        1314_701_16	272	Contig78899	2922	0	23H27M	*	0	0	GACCTTGACCTACTTTTCAATGACCTT	%+1,-6C%%.*5##7:IIIIIIIIIII	XS:A:-
        1551_763_1651	272	Contig78899	2922	0	23H27M	*	0	0	GACCTTGACCTACTTTTCAATGACCTT	"I=,2CIF>$$;>70DIIIIIIIIIII	XS:A:-
        1238_1512_669	272	Contig78899	2940	0	24H26M	*	0	0	AATGACCTTGAAAAATTATGATGAGT	IGIIIIIIIIIII==I><IIIIIIII	XS:A:-

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        • #5
          Any chance you can tell us the version you are using?

          Also, is there any parameter to make the bam store the original CS calls?
          -drd

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