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===Velvet assembling=== *Test parameters settings and k-mers: **(-short, -long) x (k-mer 21, 24, 27) *I found that k-mer 27 gave me the best result. The length setting "-long" won't work for for whole contigs dataset. Maybe these contigs are not long enough to use -long setting. *For some super long (>32kbp)contigs (like in ID3 and in ID4), I need to use "make LONGSEQUENCES" before I can run the assembly. **For super long contigs, I also tried to separate them and assembly them using mix length command -short [contigs < 32Kbp] -long [contigs > 32kbp]. There is no significant difference compared to use -short for all contigs. *Used velvet settings **velveth: k-mer 27, -short **velvetg: fixed setting as cov_cutoff 2, min-contig lgth 100 Command: samchiang@genemapster:~/Tools/velvet_1.1.03$ ./velveth /media/disk-1/samchiang/Analysis_out/velvet_test_SAG_A_ID3_K27_short 27 -fasta -short /media/disk-1/samchiang/Sub_tests_folder_imp/2_Extending_Mouse_Bac_SAG_contigs/BLAT_Meta2SAG_040311/Step4_pooled_together/SAG_A_ID3/SAG_A_ID3_and_recruted_Meta_all samchiang@genemapster:~/Tools/velvet_1.1.03$ ./velvetg /media/disk-1/samchiang/Analysis_out/velvet_test_SAG_A_ID3_K27_short/ -cov_cutoff 2 -min_contig_lgth 100 &
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