WisecondorX:bowtie2 settings

[annanever82]

I've used bowtie 2 with fast local settings but with -1 sampleR1fastq.gz and -2 sampleR2fastq.gz as input (fw and rv, paired end) and sample.sam as output
After I've used Samtools to sort and convert bam file, in this way I haven't problems to start the use of WisecondorX.

You suggest to have better results using these settings for bowtie2:

bowtie2 --local -p n --fast-local -x index -U input | bamsormadup inputformat=sam threads=n SO=coordinate outputformat=bam indexfilename=sample.bam.bai > sample.bam

1 How can I insert fw and rv fastq.gz input with -U option?
2 Can i use threads=1 as setting?
3 Sorting and conversion in bam file is made automatically with bamsormadup?