Entering edit mode
6.6 years ago
1191106787
•
0
Hi: I have a sorted and merged BAM file, and I would like to check the alignment, but the result is wrong. So, where is the problem? Thanks a lot.
The wrong result:
$ samtools tview KPGP-00001_picard_sort.bam /DataBase/Human/hg19/hg19.fa
1 11 21 31 41 51 61 71
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
samtools tview
is not the most powerful genome browser available, I would recommend IGV, IGB or Tablet (among others) to get a richer view of alignments.How is the result wrong? You mean the long stretch of Ns? Try going to some position - press
g
then write down the position, something likechr1:156000
.See some further discussion here.
all the result was only 71bp and END, but obvious human genome greater, so where is the other sequence?
hu ? kamoulox ?
XRef: https://github.com/samtools/samtools/issues/728