I'll start by saying that I am a biologist learning bioinformatics from scratch so please bear with me!
I'm doing de novo sequencing of a complex of dsRNA viruses using MiSeq 150PE reads. Some sanger sequencing has been done before so I have some partial sequences already which I'm hoping to use to validate my assemblies.
As a quick test of my new data I aligned my reads to the sanger assemblies using bowtie and used Tablet to visualise my alignments. I found that I had average read depth of 3300x to 81000x depending on the virus but sometimes the reads density was quite patchy, producing "islands" of very high coverage (suggesting that the sanger seq may not be entirely correct?).
When I produce a de novo assembly using velvet:
and then use the contigs as a reference sequence in bowtie to align the original reads, I find that I still get patchy coverage of the contigs.
How can I get patchy coverage of my velvet-derived contigs when I use the same reads to produce a bowtie alignment? Is there a better/easier way of visualising my reads on the contigs that I produce (bearing in mind that my command line skills are very basic and programming is non-existent)?
Thanks, Ed
I'm doing de novo sequencing of a complex of dsRNA viruses using MiSeq 150PE reads. Some sanger sequencing has been done before so I have some partial sequences already which I'm hoping to use to validate my assemblies.
As a quick test of my new data I aligned my reads to the sanger assemblies using bowtie and used Tablet to visualise my alignments. I found that I had average read depth of 3300x to 81000x depending on the virus but sometimes the reads density was quite patchy, producing "islands" of very high coverage (suggesting that the sanger seq may not be entirely correct?).
When I produce a de novo assembly using velvet:
Code:
velvetg Trimmed/234/_51 -cov_cutoff 10 -ins_length 170 -exp_cov 13200 -scaffolding no -min_contig_lgth 100 -unused_reads yes -read_trkg yes &
How can I get patchy coverage of my velvet-derived contigs when I use the same reads to produce a bowtie alignment? Is there a better/easier way of visualising my reads on the contigs that I produce (bearing in mind that my command line skills are very basic and programming is non-existent)?
Thanks, Ed
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