fasta support?

[scottdaniel]

I e-mailed the senior author of your paper and haven't heard back so I'm asking here...

1. Is there a way to run LSA on fasta files instead of fastq?
2. Does LSA use the quality information in the fastq files?

[brian-cleary]

Hi Scott,

Currently there is no support for fasta files. LSA does indeed use the
quality information. If you must use the fasta files, you can introduce
mock quality scores and create fastq files by giving them all high quality,
for example.

On Wed, Oct 21, 2015 at 1:50 AM, Scott Daniel [email protected]
wrote:

I e-mailed the senior author of your paper and haven't heard back so I'm
asking here...

1. Is there a way to run LSA on fasta files instead of fastq?
2. Does LSA use the quality information in the fastq files?

—
Reply to this email directly or view it on GitHub
#3.

[scottdaniel]

Ok, the reason why I want to use fasta is that I have already done QC on my fastq, split into smaller fastas and filtered for the host genome / host food (they are mice cecal matter).

Thanks for answering my question.

[scottdaniel]

By the way, how does LSA use the quality scores? Which scripts use them?

[brian-cleary]

The quality scores are incorporated when hashing the reads. So a low
quality base will hash more like an ambiguous character. This is done in
fastq_reader.py, I believe.

On Thu, Oct 22, 2015 at 6:18 PM, Scott Daniel [email protected]
wrote:

By the way, how does LSA use the quality scores? Which scripts use them?

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#3 (comment)
.