Hello,

I have used SHRiMP for aligned SOLiD RNA-Seq data using the following commands.

$SHRIMP_FOLDER/bin/gmapper-cs -N 8 --single-best-mapping -E -L $SHRIMP_INDEX/genome-8gb-12_12_12seeds-1of6-cs 1of4.csfasta > 1of4.map.db1of6.sam

and finally

$SHRIMP_FOLDER/bin/mergesam --single-best-mapping --all-contigs < `cat *of4.csfasta` `cat *of4.map.db*of6.sam` > map.sam

I expect the resulting sam/bam file to contain only uniquely mapped reads. But when I perform

samtools view -bq 1 map.sam > map_bq1.bam 
samtools view -bS map.sam > map.bam

and compare the "samtools flagstat" output for both the bam files, the map_bq1.bam gives me lesser number of reads than map.bam which is confusing because I would expect both to be the same.

Can you guys tell me why this difference occurs?

Thanks.