Using trimmed reads with HTseq-count before DESeq?

[aafc]

I am doing differential expression analysis with RNA reads.

DESeq required a count table, and I am using HTSeq to make it. My paired-end illumina reads have been trimmed, and some reads have been removed. This means that some reads do not have their mates.

I have aligned the reads using tophat, and will be converting the bam output to sam using picard-tools before I sort the output by query name. This sorted sam file will then be given to htSeq-count. The resulting count-table will be given to DeSeq.

I am wondering if the fact that some reads won't have their mate will negatively affect the results of HtSeq-count or DESeq.

Thanks.