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sfu-compbio / colormap

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Output files #4

Closed Mattstorey closed 7 years ago

Mattstorey commented 8 years ago

Hi,

Install was a piece of cake (thanks) and I ran the script on my data sets with no troubles! However, the output was not what I expected. The run returned; .iter1.fasta, .2iter.fasta and _uncorr.fasta. Are any of these the corrected files?

Cheers.

haghshenas commented 8 years ago

Hi there,

Yes, the file containing corrected reads are stored in iter2.fasta. In fact, iter1.fasta contains reads corrected by a single round of SP algorithm and iter2.fasta contains reads corrected by a second round of SP algorithm.

Mattstorey commented 8 years ago

Great. Thanks for the reply. Is there a smart way to compare the corrected reads to the uncorrected reads. Even just a subset of these. I'm interested to see how much correction has occurred?

Cheers, Matt.

On Thu, Oct 20, 2016 at 6:21 AM, Ehsan Haghshenas notifications@github.com wrote:

Hi there,

Yes, the file containing corrected reads are stored in iter2.fasta. In fact, iter1.fasta contains reads corrected by a single round of SP algorithm and iter2.fasta contains reads corrected by a second round of SP algorithm.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/sfu-compbio/colormap/issues/4#issuecomment-254881169, or mute the thread https://github.com/notifications/unsubscribe-auth/ANTnrHS-eQiZPcB66XREPTqbyGVcbvleks5q1lGJgaJpZM4KZg8x .

haghshenas commented 7 years ago

One way to compare corrected and uncorrected reads (specially for bacterial genomes) is to map them to the reference genome and calculate the identity/accuracy of the mappings. Alternatively, if you want to analyze a small subset of reads LRCstats might be a good option.