asking again about output format

[magpie]

Thank you for your quick response and sorry for bothering you.

I think my question make you be confused.
I didn't get an answer I want to know.

So, you mean I don't need to assign the output file on the command
line.
For example, 3. Usage b) command lines: from README for SOAP,
single -end alignment: soap -a query.fa -d ref.fa -o out.sop -s 12
pair -end alignment: soap -a query_1.fa -b query_2.fa -d ref.fa -o
out.sop -2 single.sop -m 100 -x 150

They assign the output format whit expansion "sop".

I was wondering if you could give me the example command line for
single-end alignment for BSMAP.

thanks,

[yxi]

Hi Magpie,

Here is an example command line for single end reads:

bsmap -a reads.fa -d ref.fa -o results.bsp -p 4 -r 0 -w 100 -s 10 -n 0
-v 2 -i 2
-p 4 use 4 cpus/cores
-r 0 only report unique mapping
-w 100 # of max multiple mapping
-s 10 seed size: 10 bp
-n 0 search both forward and reverse strand
-v 2 allow up to 2 mismatches
-i 2 using index mode 2 (only look for CG methylation)

Yuanxin