Bowtie2 Mapping Different Number Of Reads To Same Sequence When Ref-Seq Is Part Of Different Indexes

Question

[rohita.sinha]

I am using bowtie2 to map my PE reads.

I have indexed multiple bacterial genomes by putting them together in a multi-fasta file fashion.

bowtie2 -q -a -p 1 -x Multi -1 R100_1.fq -2 R100_2.fq -U 100_Orph.fastq -S 100.sam
samtools view -b -S 100.sam -o 100.bam
coverageBed -abam 100.bam -b BED_RefSeq >>100.cvg
CoverageBed ouput for genome("307679329")is :  307679329       1       25751   72      3568    25750   0.1385631

but when I index genome ("307679329") separately then CoverageBed output is:

307679329       1       25751   449     8369    25750   0.3250097

Can someone explain this differnece

Answer 1

[David Langenberger]

If I understand your data correctly, there may be some reads that have better mappings in other genomes (not 307679329). When including them, they map there and when only mapping to 307679329, they map with more errors to that genome. In a way the other genomes snatch away the reads.

May that a possibility? You can check that in the two mapping files by checking the reads together with their alignments.

Answer 2

[rohita.sinha]

Thanks for the answer. As I had opted to put "-a", I think bowtie2 should allow reads to map to all possible positions.