Aligner For Allowing Multiple Matches (#N) For A Read

Question

[Abhi]

Hi All

Based on your experience could you please recommend an aligner which can accommodate multiple read mapping positions. I have already tried BWA and Mosaik with the option to allow for multiple mappings.

With BWA I dont get the Mapping quality for all mappings and Mosaik gives me low % of reads aligned. I was wondering may be I could try something else.

Thanks! -Abhi

[lh3]

Mapping quality can only be calculated for the top hit.

Answer 1

[Leszek]

try gem-mapper

[chhylp123]

Hi, recently, I have a problem about GEM. When I want build index for human using GEM, it reported

Creating sequence and location files...
Fatal error: exception
Failure("Command 'echo "-------gem-indexer_fasta2meta+cont" > human_g1k_v37.fasta.log && gem-indexer_fasta2meta+cont -i human_g1k_v37.fasta -c dna --filter-function iupac-dna --strip-unknown-bases-threshold 50 --complement-size-threshold 2000000000 --comp.

The command I used is

./gem-indexer -i /devdata/chhy/masai/bin/human_g1k_v37.fasta -o hum.index -T 4

Could you help me to solve this problem?

Thanks!

Answer 2

[ALchEmiXt]

You can try the MUMmer suite with the maxmatch option. So allowing multiple matches. Another alternative is to simply use the fast BLAT (not BLAST) aligner.

Answer 3

[Lee Brooks]

bowtie does this beautifully.

"With the -k, -a, -m, -M, --best and --strata options, the user can flexibily select which alignments are reported"

http://bowtie-bio.sourceforge.net/manual.shtml#reporting-modes