questions about results of ubismap.py

[woooh324]

Dear @EricR86 and @mehrankr

Hello. Thank you for providing such a great program.

I have some questions about results of ubismap.py.
I've run ubismap.py with a sequence of fungi named Cryptococcus_neoformans for my metagenomics project.
There was no error but the results were not as I expected.

UniqueKmers, RunBowtie, and UnifyBowtie made their result files for every chromosome of the reference, from chr1 to chr14.

(The results of UniqueKmers and RunBowtie are not show, which are at TEMPs directory)

However, the uint8_to_bed_parallel.py only makes Single-read mappability files of chr1 and chr10. If I use Candida_albicans instead, uint8_to_bed_parallel.py only makes files of chr1 and chr2. Also, if the file is not of chr1, the same results are duplicated. For example, the result of chr10 of Cryptococcus_neoformans repeates like image below.

I'm not sure this result is reliable. Is there anything that I missed or is it just one of possible results?

I made qsub file with ubismap.py and added qsub code of uint8_to_bed_parallel.py to the file manually. To run the code, I manually changed the chromosome name of microorganism sequence from NC_* to chr*. I used k=100.

Thank you for your consideration.

[mehrankr]

Hello @woooh324

Could you please provide the command you are using for that step and ideally a reproducible example with data?

Thanks,
Mehran

[woooh324]

Dear @mehrankr

Hello @mehrankr. First of all, thanks for the quick response.

I sent you the code and example I used to run Umap of Cryptococcus_neoformans. Please take a look and let me know if you need more information.

Thank you for your help.