Chris:LabNotes/Microbiome/2013/2013-5-17: Difference between revisions

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>Cjwei
(Created page with "=Moleculo Data Analysis Part 3= *Continued from <http://genome-tech.ucsd.edu/LabNotes/index.php/Chris:LabNotes/Microbiome/2013/2013-5-15> ==Results from Test Assembly== *Previ...")
 
>Cjwei
Line 22: Line 22:
==Test Assembly + Moleculo Reads Assembly Results==
==Test Assembly + Moleculo Reads Assembly Results==
*Some basic assembly statistics:
*Some basic assembly statistics:
n      n:100  n:N50  min    median mean  N50    max    sum  
n      n:100  n:N50  min    median mean  N50    max    sum  
10322  10322  2812  1000  2458  3094  3682  17558  31.94e6 Illumina_conti
10322  10322  2812  1000  2458  3094  3682  17558  31.94e6 Illumina_conti
                                                                  g+Moleculo_ass
                                                                  g+Moleculo_ass
                                                                  embly/9-
                                                                  embly/9-
                                                                  terminator/
                                                                  terminator/
                                                                  Illumina_conti
                                                                  Illumina_conti
                                                                  g+Moleculo.scf
                                                                  g+Moleculo.scf
                                                                  .fasta
                                                                  .fasta
*CEGMA gene prediction:
*CEGMA gene prediction:
**Illumina-only assembly: [[File:2013_5_17_Test_assembly_Illumina-only.completeness_report.txt]]
**Illumina-only assembly: [[File:2013_5_17_Test_assembly_Illumina-only.completeness_report.txt]]
**Illumina+Moleculo assembly: [[File:2013-5-17_Test_assembly_Illumina+moleculo.completeness_report.txt]]
**Illumina+Moleculo assembly: [[File:2013-5-17_Test_assembly_Illumina+moleculo.completeness_report.txt]]
==Test Assembly + Moleculo Reads Assembly Conclusions==
==Test Assembly + Moleculo Reads Assembly Conclusions==
*From the Illumina-only test assembly, we found that error correction on all read files helped with assembly slightly, so we will implement error correction prior to assembly of all Illumina data
*From the Illumina-only test assembly, we found that error correction on all read files helped with assembly slightly, so we will implement error correction prior to assembly of all Illumina data

Revision as of 21:46, 26 May 2013

Moleculo Data Analysis Part 3

Results from Test Assembly

  • Previously I ran test assembly on a small subset of Illumina reads (88179998 reads) that included one 200bp library and one 2kb insert library.
  • There were three tests that I ran:
    • 1a = no error correction for any Illumina read
    • 1b = error correction only on mate-paired 2kb reads
    • 1c = error correction on all Illumina reads
  • Here are the basic assembly statistics:
n       n:200   n:N50   min     N80     N50     N20     max     sum
1772128 504382  181476  200     233     307     456     3238    156.8e6 1a_Illumina_Test_Assembly_Control/test_assembly_control.scafSeq.GC
1768536 535005  189770  200     236     313     471     4194    169.2e6 1b_Illumina_Test_Assembly_no-Mate-correction/test_assembly_1b.scafSeq.GC
1766902 535182  189131  200     236     314     475     4194    169.9e6 1c_Illumina_Test_Assembly_all-correction/test_assembly_1c.scafSeq.GC
  • Analysis: It seems as though having error correction on all reads provided slightly better assembly results, so I'll apply error correction on all Illumina reads for downstream assembly

Test Assembly + Moleculo Reads Assembly

  • Ran hybrid assembly on genemapster </media/disk-2/cjwei/130419_Oncomelania_Illumina_Moleculo/Illumina_contigs+Moleculo_Assembly>
  • Commands/instructions to run:
    • Make frg files for combined Illumina test assembly scaffolds + Moleculo data (411,392,248bp), in 1_frg.sh file
/media/2TB_store1/cjwei/software/Hybrid_error_correction_assembly_software/wgs_download_2/wgs-7.0/Linux-amd64/bin/fastqToCA -libraryname illumina_contigs_moleculo -reads Illumina_contig+Moleculo.fastq >Illumina_contig+Moleculo.frg
    • Run assembly, in 2_runCA.sh file
~/software/Hybrid_error_correction_assembly_software/wgs-7.0/Linux-amd64/bin/runCA -d Illumina_contig+Moleculo_assembly -p Illumina_contig+Moleculo Illumina_contig+Moleculo.frg

Test Assembly + Moleculo Reads Assembly Results

  • Some basic assembly statistics:
n       n:100   n:N50  min    median mean   N50    max    sum 
10322   10322   2812   1000   2458   3094   3682   17558  31.94e6 Illumina_conti
                                                                  g+Moleculo_ass
                                                                  embly/9-
                                                                  terminator/
                                                                  Illumina_conti
                                                                  g+Moleculo.scf
                                                                  .fasta

Test Assembly + Moleculo Reads Assembly Conclusions

  • From the Illumina-only test assembly, we found that error correction on all read files helped with assembly slightly, so we will implement error correction prior to assembly of all Illumina data
  • From the Illumina+Moleculo assembly, we concluded:
    • Adding Moleculo data drastically increases the scaffold size, while reducing the sum bp assembled (most likely because the shorter Illumina scaffolds are discarded)
    • While the CEGMA results show very few genes predicted from the core eukaryotic gene set, we notice that Illumina+Moleculo data has a few complete genes mapped. This may be because of the longer scaffold size.
  • I'm going to move forward with assembly of all of the Illumina data combined and hybrid assembly of those scaffolds with Moleculo data