Mapping to SOLiD reads to draft genome

[saha]

I am presently involved in hybrid assembly and want to map my SOLiD reads against ROCHE contigs (length more than 1000bp). I approach is to map the reads with corona_lite, but facing problem with the cmap file. I found a small paragraph regarding this particular situation in corona_lite documentation but it is not that illustrative. Usually for mapping against human genome we take cmap as follows:

1 1 path to reference for each chr. path to the double encoded file

But for a draft genome i am confused. it tried with this following approach but i failed. i present cmap that i tried was:

1 contig0001 path to the multifasta contig file

Any help and guidance will be appreciable.

with regards,
saha

[westerman]

Either make a very large cmap file with one line per contig file. Or put all of the contigs into one file and separate them by 'N's; that is the file will look like one large sequence. I usually do the latter. If you are clever with how many N's you use to separate each contig then you can get information from the mapping file; e.g., map to bases 1-1323 means contig#1, bases 1500-2300 contig #2, etc.