[Bio-bwa-help] BWA mem alignment to duplicated regions

[Anne B. <pl...@no...>]

I have aligned Illumina paired-end ChiP-seq reads using BWA-mem. The reference genome has a duplicated region on chromosomes 2 and 4. When I count the number of reads aligned to each of the regions I get a different number. If BWA-mem align the reads randomly on duplicated regions wasn't I supposed to get the same number of reads for each duplicated region?


The regions are 8kb long and flanked by the same sequences where my tagged protein doesn't bind so I would not expect uniquely alignment for any of the sequences.
It is crucial for me to understand the reason for this discrepancy, so I would appreciate a lot any help.


bwa mem -B 40 -O 60 -E 10 -L 50 -M -R '@RG\tID<http://gatkforums.broadinstitute.org/gatk/profile/RG%5CtID>:WTCHG_261086_294\tSM:WTCHG_261086_294' -t 10 /home/plxacb/Fixed_fasta/Ade_fasta/Cen8Ade6.fa WTCHG_261086_294.unmapped_ecoli_1.fastq WTCHG_261086_294.unmapped_ecoli_2.fastq | samtools view -bS - > WTCHG_261086_294.strict_bwamem.bam


samtools view WTCHG_261086_294.strict_bwamem.sorted.bam Not76_Chr2_ref:125168-133320 | wc -l

222754


samtools view WTCHG_261086_294.strict_bwamem.sorted.bam Not76_Chr4_ref:1619693-1627845 | wc -l

271688




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