Bowtie2 reporting alignments count

I am using bowtie2 for mapping genome to reference fasta. As said in bowtie2 manual it reports only the best one alignment. What if read has two best alignments with the same score? Will it report only one random read?

genome alignment

• 3,041 views • link

updated 4.0 years ago by Ram

• written 10.7 years ago by bbb •

1 answer

Hi,

Yes, bowtie2 will report a random position for a read (among the best positions) if there are more available position than the requested number. You can modify the maximum amount of position per read. Have a look over here :)

• 0 views • link

written 10.7 years ago by Thibault D.

More posts like this

Bowtie alignment reporting
written 6.0 years ago by VineethVenumadhavan •

What is the difference between bowtie alignment reporting options I) `-k 1` and II) `-a --best --strata` Both reports best one alignment ? If not …
HISAT2 -k option
written 6.4 years ago by dklinkebiel •

When setting the HISAT2 alignment option -k to one (1), does that mean that it will only report the the Primary alignment with the best …
Getting Bowtie2 or BWA to output more than one top alignment (not just a random one)
written 7.1 years ago by anm5579 •

I want to find multi-mapped reads in my data. In general, if a read maps to multiple positions with the same mapping score, I want …
ambiguous characters are not reported in Bowtie2 alignments
written 7.2 years ago by Famf •

I am trying to align a set of read sequences (SNP chip array) to a reference genome. I want to get the physical positions of …
Bowtie2 reports no secondary alignments
written 7.7 years ago by goodez

This has been bugging me for awhile now. I know there are multiple mapping reads in my alignments, but bowtie2 does not assign the 256 …
STAR unique reads
written 8.6 years ago by TEman •

In STAR, one can use the --outFilterMultimapNmax 1 to report only reads that map exactly one time to the reference genome. This can be useful …
Finding alignment score for multi-read frombam/sam file
written 10.0 years ago by EVR

Hi, I have mapped my RNA seq reads to the genome using tophat2. Thought eh mapping rate was 80%, it has been reported ~35 % …
Tophat And Multiple-Mapped Reads
written 13.3 years ago by Biomonika (Noolean)

I would like to ask about update on this topic: <a href='http://seqanswers.com/forums/showthread.php?t=24270'>http://seqanswers.com/forums/showthread.php?t=24270</a> <pre><code>-g/--max-multihits <int> Instructs TopHat to allow up to this many alignments to the …
Why Is Tophat Reporting Secondary Alignments Even When The Option To Do So Is Turned Off
written 13.5 years ago by Varun Gupta

Hi Everyone I am working with Rna seq data and for that i am using TOPHAT aligner. I came across 2 options in tophat which …
Does Bowtie2 Map Multiple Reads To The Same Gene?
written 13.7 years ago by derekc10741 •

Hi all, I'm new to bioinformatics and I've a question about bowtie2. I know that bowtie2 reports read that map to the reference genome, but …