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philres / ngmlr

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations
MIT License
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Documentation for Progress Info #24

Closed nathanhaigh closed 6 years ago

nathanhaigh commented 7 years ago

I'm using ngmlr for the first time....easy installation and easy to run. However, I don't know what all the information means in the reported progress info. Some documentation around this would be useful.

For example, my progress is currently showing:

Processed: 92198 (0.66), R/S: 37.44, RL: 8857, Time: 2.00 5.00 11.62, Align: 0.96, 490, 0.81
philres commented 7 years ago

92198 reads were processed so far 66 % of the 92198 reads were mapped (with > 25 % of their bp mapped) 37.44 are mapped on average per second 8857 is the average read length so far

"Time" only gives you a rough estimate on how much time is spent on the three major parts of the mapping process (subread mapping, subread merging and convex sequence alignments). This is actually only interesting for development and will be removed at some point

"Align" is also more of an internal sanity check. It tells you that 96 % of the attempted alignments could be completed on the first try. The other 4 % had to be recomputed because the initial alignment band was too small. 490 is the average width of the alignments band. The last number tells you that on average 81 % of the bp of a read were mapped

As I said "Time" and "Align" are pretty much only for debugging purpose and will sooner or later be removed.

Hope that helped. I'll also add documentation about this to the readme file. Let me know if you want to know anything else.

Philipp

nathanhaigh commented 7 years ago

That's all good! The inclusion of this info in the readme would work be great!

Nastiya commented 6 years ago

Hi , Thanks for the explanation, but I got lost as well. I run it for the first time, and as an output I've received two .ngm files. How can I open these files, and where I can see the mapping of the mapped reads to my reference sequence. Thanks

fritzsedlazeck commented 6 years ago

Hi Nastiya, when you run ngm did you include reads? If you jus see the two .ngm files these are just the indexes from your reference. Please look at the readme with the information on how to run it. Thanks Fritz

Nastiya commented 6 years ago

Dear @fritzsedlazeck , Thank you for the quick reply. I indeed received 3 files: 2 .ngm files and on .sam file. Now, I'm trying to use Tablet to visualize it. I'm inserting .sam file as the assembly, but get an error of the reference file. Should I use one of these .ngm files as a reference instead of the original ref.fasta file I've used when running the ngmlr command?

Best. A

fritzsedlazeck commented 6 years ago

Dear Nastiya, please read the documentation of tablet. You certainly need to convert sam -> bam and sort it. (e.g. using samtools). You probably need further to index the reference file. This is unrelated to NGM so please contact them for support or read their documentaton. Thanks Fritz