Mosaik-aligner for SNP detection, Need Help.

[ketan_bnf]

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)

[ntremblay]

Hi,

when your are building the dat file specifying your input FASTQ?

you shouldn't see the c.elegans file in the ace file you're getting!

Do you see all your reads stats in the post build/assembly report?

[ketan_bnf]

yes, i am using FASTQ file for dat file formation.

yes, you are right i should not see c.elegans file in the ace file and i am not seeing it as well.

I am not merging c_elegans data with my data, i just meant to say processing of my data with mosaik-aligner dosen't give output as it gives with test data of c_elegans .

I am pasting my stats of post align/assembly report.

1. orf@ubuntu:~/mosaik-aligner/data$ ../bin/MosaikAligner -in sequence_archives/454AllContigs_normal.dat -out sequence_archives/454AllContigs_normal_chr5_aligned.dat -ia reference/chr5.dat -hs 13 -act 55 -mmp 0.05 -bw 51 -mhp 100

MosaikAlign gives output showing,

Alignment statistics (mates):
===================================
# filtered out: 3804 ( 92.9 %)
# unique: 123 ( 3.0 %)
# non-unique: 168 ( 4.1 %)
-----------------------------------
total: 4095
total aligned: 291 ( 7.1 %)

Miscellaneous statistics:
==================================
aligned mate bp: 95883
alignment candidates/s: 854.4

2. orf@ubuntu:~/mosaik-aligner/data$ ../bin/MosaikSort -in sequence_archives/454AllContigs_normal_chr5_aligned.dat -out sequence_archives/454AllContigs_normal_chr5_sorted.dat

MosaikSort gives output showing,

Single-end read statistics:
======================================================
reads alignments
------------------------------------------------------
# non-unique: 168 (57.7 %) 20932 (99.4 %)
# unique: 123 (42.3 %) 123 ( 0.6 %)
------------------------------------------------------
total: 291 21055

[test@BIOTECH-PC-1 data]$ ../bin/MosaikText -in sequence_archives/454AllContigs_normal_chr5_sorted.dat -ref chr5 -bam bam/454AllContigs_normal_chr5.bam
------------------------------------------------------------------------------
MosaikText 1.0.1388 2010-02-01
Michael Stromberg Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- converting the alignment archive to the following formats: BAM

Converting alignment archive:
100%[================================] 123.0 alignments/s in 1 s


[test@BIOTECH-PC-1 data]$ ../bin/MosaikAssembler
-in sequence_archives/454AllContigs_normal_chr5_sorted.dat -out assembly/chr5/454AllContigs_normal_chr5_sorted -ia reference/chr5.dat -f ace
./Assemble.sh: line 1: #!/bin/sh: No such file or directory
------------------------------------------------------------------------------
MosaikAssembler 1.0.1388 2010-02-01
Michael Stromberg Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

===============================================================
alignment count reference sequence
---------------------------------------------------------------
123 chr5

Processing reference sequence chr5:
- inserting gaps into reference sequence... finished.
- creating ungapped to gapped conversion table... finished.
- writing assembly header... finished.
- locating first read for this reference sequence... finished.

- saving alignments from chr5:
100%[================================] 123.0 alignments/s in 1 s

- appending read data to header data... finished.



Whether i should use contigs or reads for aligning?