parser for sam?

[bioinfo308]

hello all

I'm newbie and need advices..

this is my first post here in seqanswers. help me out.

what i'm trying to do is find DEGs in differently stress-treated groups.

what i have been done are like this...

i have raw seqs from 454 and sanger of each stress group.

i've done pre-processing job so they are ready to be assembled.

i combined clean reads of each group into one fasta file then i ran iAssembler.

iAssembler gave me sam file and consensus file as an ouput.

what i want to do is

extract origin of reads distribution from unigene..

like unigene one consists # of reads from stress group 1, # of reads from stress group2.. and so forth..

not sure that i made myself clear. forgive my poor english

want to know is this possible what i'm trying to do?

and is there any parser that can achieve what i'm trying to do?

thank you guys in advance.

[TiborNagy]

Hi.
Why do you combine stress-treated groups? You can run iAssembler in each groups.
If there is a special reason to combine the reads, you can add tags to the read names using sed Linux command. After that you can easily identify your reads in the final SAM file.