Need help!
I am using Mosaik-aligner on ubuntu-9.10 for SNP detection, it operates without showing any errors. I have 454 sequencing data and i am using contigs formed by gsAssembler software that is available with 454 titanium system, formed from reads,
Steps for using Mosaik-aligner are,
./MosaikBuild (.fastq and ref.fasta)
./MosaikAlign (using parameters -hs 14 -mmp 0.05 -act 55 -bw 51 -mhp 100 for 454)
./MosaikAssmeble
at the end i get *.ace file which i tried to open in Tablet, Gambit etc but it is not showing any alignments as it shows with the test data (c_elegans) given with mosaik. It shows how much sequences has aligned to me ref seq uniquly and non-uniquly but in .ace file no data except ref seq is seen.
*.bed and *.eland files shows contigs/reads aligned to my reference derived using MosaikText.
If any one knows the solution pls help me i am stucked here?
Whether i should use reads (from which contigs are formed) instead of contigs? (which i have did but the result is same, nothing seen)
I am using Mosaik-aligner on ubuntu-9.10 for SNP detection, it operates without showing any errors. I have 454 sequencing data and i am using contigs formed by gsAssembler software that is available with 454 titanium system, formed from reads,
Steps for using Mosaik-aligner are,
./MosaikBuild (.fastq and ref.fasta)
./MosaikAlign (using parameters -hs 14 -mmp 0.05 -act 55 -bw 51 -mhp 100 for 454)
./MosaikAssmeble
at the end i get *.ace file which i tried to open in Tablet, Gambit etc but it is not showing any alignments as it shows with the test data (c_elegans) given with mosaik. It shows how much sequences has aligned to me ref seq uniquly and non-uniquly but in .ace file no data except ref seq is seen.
*.bed and *.eland files shows contigs/reads aligned to my reference derived using MosaikText.
If any one knows the solution pls help me i am stucked here?
Whether i should use reads (from which contigs are formed) instead of contigs? (which i have did but the result is same, nothing seen)
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