Trouble with uniquely mapped reads about midas HOT 3 CLOSED

Hi nafeesatk,

Everything you've done looks correct. However, I've run that same sample through MIDAS and get several hundred uniquely reads mapped to the marker genes.

I think the easiest solution would be for me to recreate the issue on my system using your FASTQ file. If you send me your email address, I can send a dropbox link where you can upload your FASTQ.

Thanks,
Stephen

from midas.

Hi Stephen,

Thank you so much for your help! My email is [email protected].

Best,

Nafeesa

from midas.

Hi Nafeesa,

I see the issue now. It appears you have merged read1 and read2 from SRR1927149_1.fastq and SRR1927149_2.fastq.

For most Illumina libraries read1 and read2 occur about 350 bp apart. So you won't get an alignment that covers the entire read, because in reality, there is a big gap between them. MIDAS sees that the alignments only cover a portion of the read and is therefore throwing them out.

I would strongly recommend running MIDAS without merging your reads. But if this is not possible, you can try decreasing the value for --aln_cov. The default if 0.7, but you can try dropping it to 0.35.

Best,
Stephen

from midas.