search

merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
427 stars 145 forks source link

number of reads mapped for each profile in the summary output #507

Closed tdelmont closed 7 years ago

tdelmont commented 7 years ago

I recently learned that only 40% of my issues are being considered, yet I am trying my chances once again.

Would be great to summarize the number of reads/profile in the summary.

Tom

ziels commented 6 years ago

Hi! I see that this issue is closed, but I am wondering if it was resolved? I too, am looking for the number of reads mapped per bin in the summary output, but I can't seem to find it (only coverage values per bin). Is the number of mapped reads per bin output anywhere in the summary?

Thanks! Ryan

luuuuuuuke commented 6 years ago

Hey Ryan, It doesn't look like read # is available in the summary output. However, a roundabout method would be to use anvi-get-short-reads-from-bam and pass your collection name (or bin name if you prefer). This will output a fasta file of the short reads contributing to the collection and you can then do a simple grep (grep '>' shortreads.fasta | wc -l) to count the number of '>' in the file, which will give you the # of short reads in the collection.

However, if you want this divvied up across samples I don't think that method will work :/. Maybe somebody has a better method to find # of short reads in bins across samples?

-Luke

On Mon, Nov 27, 2017 at 11:33 AM, ziels notifications@github.com wrote:

Hi! I see that this issue is closed, but I am wondering if it was resolved? I too, am looking for the number of reads mapped per bin in the summary output, but I can't seem to find it (only coverage values per bin). Is the number of mapped reads per bin output anywhere in the summary?

Thanks! Ryan

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/merenlab/anvio/issues/507#issuecomment-347279555, or mute the thread https://github.com/notifications/unsubscribe-auth/AY6jPGQnATtk63uu2T-IikA4HjkGCBWNks5s6wB7gaJpZM4NMbQP .

-- Dr. Luke McKay

Postdoctoral Research Scientist Department of Land Resources and Environmental Sciences (815 LJH) Center for Biofilm Engineering (313 Barnard Hall) Montana State University