output file format for bsmap

[magpie]

Hello,

I have to say "thanks" first.
I'm trying to analyze my data using BSMAP.
Even though I read the paper and some introduction from README, I
don't know the output file format.
I wrote on the command line the following:
./bsmap -a inputfile(read).fa -d inputfile(reference).fa -o
outputfile.&&&
Is there any wrong command on it? If so, could you tell me how can I
correct them and output file format?

I'm not familiar with SOAP and I just read the introduction for SOAP
which you attached.

Thanks.

[Yuanxin Xi]

Hi Magpie,

Thanks for your interests in BSMAP.

The output format is described in the README

***********************************************
4. Output

BSMAP output the mapping results in the following format:

id, seq, qual, #hits, a/b, length, +/-, ref, ref_location, mismatches_info

id: readid
seq: mapped read sequence
qual: mapped read quality
hits: number of hits
a/b: which end(only meaningful for pair-end mapping)
strand:
++: forward strand of Watson of reference (BSW)
+-: reverse strand of Watson of reference (BSWC)
-+: forward strand of Crick of reference (BSC)
--: reverse strand of Crick of reference (BSCC)
ref: reference sequence name
ref_location: mapping coordinate (1 based, 5'-end coordinates of the
mapping region on the Watson reference)
mismatch_info: #mismatches_of_current_hit, #0_misatch_hits,
#1_mismatch_hits, #2_mismatch_hits, ..., #n_mismatches

each field is separated by TABLE delimiter.

***********************************************

There are other parameters you may find relevant to your study in the
README file, like -s seed -i indexmode, etc

Thanks,

Yuanxin