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==Background== *Sam tried to increase SAG contig length by using recruited sequences from metagenomic contigs (http://genome-tech.ucsd.edu/LabNotes/index.php/Sam:LabNotes/Microbiome-new/2011-4-19) **But results showed some decreased contig lengths after recruitment (ID2, ID9, ID11) **Dr. Zhang suggested that the decreased contig lengths may be fixed by slide shortening of contigs *On 4/29, I wrote perl script that could help perform the slide shortening of contigs *Here, I test the script/method of slide shortening to increase the contig length after recruitment *SAG sequence: ID9 because showed the lower contig length but showed relatively good contig length **Sequences found in: </media/disk-1/samchiang/Sub_tests_folder_imp/2_Extending_Mouse_Bac_SAG_contigs/BLAT_Meta2SAG_040311/Step4_pooled_together/SAG_A_ID9> **Test found in: </media/disk-2/cjwei/slide-shortening_Assembly_Test> **Used various sliding cut lengths: ***Test 1: >1000bp contigs cut; step size = 200bp ***Test 2: >2000bp contigs cut; step size = 100bp (same as "Whole Genome Amplification and Denovo Assembly of Single Bacterial Cells") ***Test 3: >1000bp contigs cut; step size = 100bp ***Test 4: >100bp contigs cut; step size = 10bp (most highly cut option) ***Test 5: No sliding cut but have assembly ***Test 6: Control (no sliding cut, no assembly -> just run abyss-fac on the combined file) ***Test 7: SAG contigs (for comparison to determine if recruitment helped) *Also tried out the sliding cut on another assembly (see if can improve the average recruited assembly results) = ID1 **Test 1: >2000bp contigs cut; step size = 100bp (was shown with ID9 that this produced highest N50 and highest sum) **Test 2: No sliding cut but have assembly **Test 3: Control (no sliding cut, no assembly -> just run abyss-fact on the combined file) **Test 4: SAG contigs (for comparison to determine if recruitment helped)
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