Chris:LabNotes/Moleculo/2013/2013-5-17
Jump to navigation
Jump to search
Moleculo Data Analysis Part 3[edit]
- Continued from <http://genome-tech.ucsd.edu/LabNotes/index.php/Chris:LabNotes/Microbiome/2013/2013-5-15>
Results from Test Assembly[edit]
- 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[edit]
- Ran hybrid assembly on genemapster </media/disk-2/cjwei/130419_Oncomelania_Illumina_Moleculo/Triton_Hybrid_Assembly_5_13_2013/test_assembly+moleculo>
- Commands/instructions to run:
- Make frg files for combined Illumina test assembly scaffolds (test 1c) + Moleculo data (411,392,248bp)
/media/2TB_store1/cjwei/software/Hybrid_error_correction_assembly_software/wgs_download_2/wgs-7.0/Linux-amd64/bin/fastqToCA -libraryname test_assembly_moleculo -reads test_assembly+moleculo.fastq >test_assembly+moleculo.frq
- Run assembly
/media/2TB_store1/cjwei/software/Hybrid_error_correction_assembly_software/wgs-7.0/Linux-amd64/bin/runCA -d test_assembly_moleculo -p test_assembly_moleculo test_assembly+moleculo.frg
Test Assembly + Moleculo Reads Assembly Results[edit]
- 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
- CEGMA gene prediction:
- 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
Test Assembly + Moleculo Reads Assembly Conclusions[edit]
- 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