methplotlib
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wdecoster
Remora .bam as a input
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.
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.
