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?
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by damiankao View PostDoes 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?
-
Originally posted by damiankao View PostDoes 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?
Can you dump some entries from your BAM?-drd
Comment
-
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
Latest Articles
Collapse
-
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...-
Channel: Articles
03-22-2024, 06:39 AM -
-
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...-
Channel: Articles
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
by seqadmin
03-27-2024, 06:37 PM
|
||
Started by seqadmin, 03-27-2024, 06:07 PM
|
0 responses
11 views
0 likes
|
Last Post
by seqadmin
03-27-2024, 06:07 PM
|
||
Started by seqadmin, 03-22-2024, 10:03 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
03-22-2024, 10:03 AM
|
||
Started by seqadmin, 03-21-2024, 07:32 AM
|
0 responses
69 views
0 likes
|
Last Post
by seqadmin
03-21-2024, 07:32 AM
|
Comment