What steps will reproduce the problem?
I am aligning reads with 2 different scenarios:
1) align reads to a FASTA with a single reference sequence (ie. multiple reads
should almost never happen)
2) align reads to a FASTA with many highly related reference sequences (ie.
multiple reads are common)
What is the expected output? What do you see instead?
I am hoping that I can find some way such that either route will generate a BAM
that contains all primary and supplemental alignments. According to this post:
https://code.google.com/p/mosaik-aligner/issues/detail?id=116&q=multiple
I expected the primary BAM would always contain all alignments. However, what
I am finding is that no matter what parameters I use the primary BAM seems to
contain only 1 alignment per read. the multiple BAM contains all alignments,
but it only contains alignments for reads with multiple hits (ie. wont include
a read if it happened to have a single hit).
What version of the product are you using? On what operating system?
I see this on RHEL and ubuntu, using mosaik 2.1.74
Thank you for any help.
Original issue reported on code.google.com by bbimber@gmail.com on 25 Feb 2015 at 1:53
Original issue reported on code.google.com by
bbimber@gmail.comon 25 Feb 2015 at 1:53