Chris:LabNotes/Microbiome/2011/2011-5-2: Difference between revisions

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  7861    7861    726    100    196    469    1039  21081  3689257 contigs_1000_100.fa
  7861    7861    726    100    196    469    1039  21081  3689257 contigs_1000_100.fa
  7869    7869    718    100    196    468    1041  21091  3690448 contigs_100_10.fa
  7869    7869    718    100    196    468    1041  21091  3690448 contigs_100_10.fa
990    990    101    100    211    505    980    19794  500631  SAG_A_ID9_and_recruted_Meta_all_Assembly
  14828  14828  1140  100    170    403    902    38317  5988190 ../SAG_A_ID9_and_recruted_Meta_all
  14828  14828  1140  100    170    403    902    38317  5988190 ../SAG_A_ID9_and_recruted_Meta_all
*Based on results, notice that >2000bp contigs cut; step size = 100bp had highest N50 and sum (with relatively the same number of contigs formed -> slightly fewer may be because less short contigs?)
*Based on results, notice that >2000bp contigs cut; step size = 100bp had highest N50 and sum (with relatively the same number of contigs formed -> slightly fewer may be because less short contigs?)
===ID3 (best assembly)===
===ID3 (best assembly)===
  n      n:100  n:N50  min    median mean  N50    max    sum
  n      n:100  n:N50  min    median mean  N50    max    sum
  1818    1818    123    100    276    1270  4712  54000  2309329 contigs.fa
  1818    1818    123    100    276    1270  4712  54000  2309329 contigs.fa
  6232    6232    471    100    276    2816  10646  54047  17.55e6 ../SAG_A_ID3_and_recruted_Meta_all
  6232    6232    471    100    276    2816  10646  54047  17.55e6 ../SAG_A_ID3_and_recruted_Meta_all

Revision as of 21:52, 2 May 2011

Slide Shortening Assembly Test

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)
  • Also tried out the sliding cut on best assembly (see if can improve the best recruited assembly results) = ID3
    • Tested >2000bp contigs cut; step size = 100bp (was shown with ID9 that this produced highest N50 and highest sum)

Procedure

  • Use Sliding Cut for combined SAG and recruited metagenome contigs:
perl contig_sliding_cut.pl SAG_A_ID9_and_recruted_Meta_all >SAG_A_ID9_and_recruted_Meta_all_slide_cut
  • Run Velveth
    • k-mer 27, -short
/media/disk-2/cjwei/Velvet/velveth SAG_A_ID9_and_recruted_Meta_all_slide_cut_Assembly/ 27 -fasta -short SAG_A_ID9_and_recruted_Meta_all_slide_cut
  • Run Velvetg
    • fixed setting as cov_cutoff 2, min-contig lgth 100
/media/disk-2/cjwei/Velvet/velvetg SAG_A_ID9_and_recruted_Meta_all_slide_cut_Assembly/ -cov_cutoff 2 -min_contig_lgth 100

Results

ID9 (problem assembly)

n       n:100   n:N50  min    median mean   N50    max    sum
7871    7871    737    100    196    465    1000   20981  3662057 contigs_1000_200.fa
7819     7819    710    100    197    473    1057   21081  3703868 contigs_2000_100.fa
7861    7861    726    100    196    469    1039   21081  3689257 contigs_1000_100.fa
7869    7869    718    100    196    468    1041   21091  3690448 contigs_100_10.fa
990     990     101    100    211    505    980    19794  500631  SAG_A_ID9_and_recruted_Meta_all_Assembly
14828   14828   1140   100    170    403    902    38317  5988190 ../SAG_A_ID9_and_recruted_Meta_all
  • Based on results, notice that >2000bp contigs cut; step size = 100bp had highest N50 and sum (with relatively the same number of contigs formed -> slightly fewer may be because less short contigs?)

ID3 (best assembly)

n       n:100   n:N50  min    median mean   N50    max    sum
1818    1818    123    100    276    1270   4712   54000  2309329 contigs.fa
6232    6232    471    100    276    2816   10646  54047  17.55e6 ../SAG_A_ID3_and_recruted_Meta_all