Do I need remome the reads aligned >1 times and how?

[wmseq]

Hi every one,
I am trying to identify the up-regulated or down-regulated genes by a compound. Here is the results of alignments for one control with different parameters.

$~/my_rnaseq_dat$ ~/bin/bowtie2 -p 8 --sensitive -x Amhg45 -U ~/sequencing_data2013/CK_2.fastq -S CK_2.sam
56874766 reads; of these:
56874766 (100.00%) were unpaired; of these:
9752857 (17.15%) aligned 0 times
43225883 (76.00%) aligned exactly 1 time
3896026 (6.85%) aligned >1 times
82.85% overall alignment rate

$~/my_rnaseq_dat$ ~/bin/bowtie2 -p 8 --very-sensitive -x Amhg45 -U ~/sequencing_data2013/CK_2.fastq -S ~/sequencing_data2013/CK_2.sam
56874766 reads; of these:
56874766 (100.00%) were unpaired; of these:
9695758 (17.05%) aligned 0 times
43182043 (75.92%) aligned exactly 1 time
3996965 (7.03%) aligned >1 times
82.95% overall alignment rate

Althoug I changed the parameter, I could not inrease the percent of the reads aligned exactly 1 time and decrease the percent of the reads aligned >1 times.

Can I used them for the following analysis? If they could not be used, how can I remove it from the sam file?

Thanks a lot?

Richard

[westerman]

Best bet is to not use any reads with a low MAPQ (mapping quality). This will include multiply aligned reads. samtools gives you a way to filter out low MAPQ reads.

[Dario1984]

There's no reason to think that reads which map multiply are bad. Genes share common domains. You could try Cufflinks, which can use these reads to improve transcript estimates.