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Hi All,
My n50 sizes are significantly smaller after running Oases when compared to the N50 of the contigs.fa file that I generated using Velvet. For example, for kmer size 63 the N50 value of the contigs.fa file is 1177 bp, using this velvet assembly I ran Oases and got an N50 value of 606 bp. Anyone ever see this and know why this can happen? I've always had larger N50 values after running Oases. I tested a range of kmer values from 31 - 69 in Velvet and selected 63 because it produced the highest N50 value. Below is a summary of my procedure:
1. FastX_trimmer
2. Cutadapt
3. fastq_quality_filter (filter low quality reads)
4. fastx_artifact_filter
5. sync files and shuffle
6. submit shuffled file to Velvet. Ran kmers 31 - 69.
7. Select best kmer by which produced the highest n50 contig size.
8. Used that kmer velvet assembly to run Oases.
9. calculate n50 value of transcripts.fa file
What am I doing wrong?!?
Thank you for your help!
Veronica
My n50 sizes are significantly smaller after running Oases when compared to the N50 of the contigs.fa file that I generated using Velvet. For example, for kmer size 63 the N50 value of the contigs.fa file is 1177 bp, using this velvet assembly I ran Oases and got an N50 value of 606 bp. Anyone ever see this and know why this can happen? I've always had larger N50 values after running Oases. I tested a range of kmer values from 31 - 69 in Velvet and selected 63 because it produced the highest N50 value. Below is a summary of my procedure:
1. FastX_trimmer
2. Cutadapt
3. fastq_quality_filter (filter low quality reads)
4. fastx_artifact_filter
5. sync files and shuffle
6. submit shuffled file to Velvet. Ran kmers 31 - 69.
7. Select best kmer by which produced the highest n50 contig size.
8. Used that kmer velvet assembly to run Oases.
9. calculate n50 value of transcripts.fa file
What am I doing wrong?!?
Thank you for your help!
Veronica