Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

    Comment


    • #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

      Comment


      • #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:-

        Comment


        • #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

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Strategies for Sequencing Challenging Samples
            by seqadmin


            Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
            03-22-2024, 06:39 AM
          • seqadmin
            Techniques and Challenges in Conservation Genomics
            by seqadmin



            The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

            Avian Conservation
            Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
            03-08-2024, 10:41 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 03-27-2024, 06:37 PM
          0 responses
          12 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-27-2024, 06:07 PM
          0 responses
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-22-2024, 10:03 AM
          0 responses
          53 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 03-21-2024, 07:32 AM
          0 responses
          69 views
          0 likes
          Last Post seqadmin  
          Working...
          X