Remora .bam as a input
Fatihlrcfs opened this issue · 7 comments
Hi @wdecoster ,
This is not for error/issue. I am just wondering whether can I use the remora .bam file (MM/ML tag) as input. Also, I could not see the bam input option in the help options. thanks .:)
Yes, I did implement support for bam,cram with MM/ML tags, but I have to admit that is insufficiently tested. Feedback is therefore appreciated. The file format is recognized, so you don't need a specific input option.
Hi @wdecoster ,
I have 2 versions of methplotlib in 2 different env. I used methplotlib -m age21bc15.sorted2_mapped.bam -n age21freqquency -w 15:23000000-25500000 -g gencode.v39.annotation.gtf.gz command. The version 0.8.0 got the error? below
Input file age21bc15.sorted2_mapped.bam not recognized! File "pandas/_libs/parsers.pyx", line 544, in pandas._libs.parsers.TextReader.cinit
File "pandas/_libs/parsers.pyx", line 633, in pandas._libs.parsers.TextReader._get_header
File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 1952, in pandas._libs.parsers.raise_parser_error
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
Then ı tried the same command in version 0.20.1 and got some graph below
Found 0 transcript(s) in the region.
Found 0 transcript(s) in the region.
Found 0 transcript(s) in the region.
Well it probably wasn't supported yet in the older version.
yes you are right ı tried to see what come up and inform you about the previous version. Also, the latest version looks working but lots of red is normal? thanks
hi @wdecoster
I generate 2 graphs (one from nanopolish and one from remora with the same data set) and you can see the below.
@wdecoster I'm wondering if this has been addressed further as I'm also interested in using what is now the official base caller's output (dorado) with your tool.
Thanks for reminding me. I will follow up on this, probably next week.