About SOAP2

[hus]

Hello,

Im learning to use SOAP2 currently.
Ive manage to build the 13 index files using chr1.fa

So now i want to test run the alignment quick start using this:
./soap –a <reads_a> -D <index.files> -o <output></output>

from where should i get the reads_a (should i put the chr1.fa file in same directory as soap & 2bwt-builder?) & which index.files to use?

What im trying to do is to align the refseq chr1.fa with the same seq chr1.fa. so i would get 100% alignment, right?

Your reply is much appreciated. TQ

[mitochy]

Hi!

1. About index:
For example your index is named "chr1.fa"
Therefore your index is "chr1.fa.index"
So type "-D chr1.fa.index"

2. About reads:
I do not think that aligning chr1.fa with chr1.fa will work because it has the wrong format (you could try though). reads_a is usually in fastQ file (fastQ, not fastA). E.g. http://maq.sourceforge.net/fastq.shtml
However, you could turn your chr1.fa into chr1.fq by doing this:
a. make new text file, name it chr1.fq
b. open chr1.fa, copy ALL sequence excluding the name (the very first line that start with ">")
c. now edit chr1.fq and enter these 4 lines (paste your sequence at 2nd line)

@CHR1.fq
paste sequence here
+
55555555555555555555555555555

d. you see those "5s" at the last line? Put as many "5" as the number of basepair of your sequence (e.g. you have 4500000 basepair sequence, put 4500000 "5")

[hus]

Hi mitochy!

thanks alot for the reply.

any quick& accurate way to put the 5s? bcos ive counted the bps of chr1. its 249250621 !

[hus]

Ahh & 1 more thing is the output.

./soap –a <reads_a> -D <index.files> -o <output></output>

what should i put in there?