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gaoyubang / nanom6A

MIT License
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query regarding output file #15

Closed aman21392 closed 2 years ago

aman21392 commented 2 years ago

In the genome_abandance.x.bed file:- chrom | coordinate | gene | read id | read pos | kmer chr7 | 5567320 | ACTB | e88129423ae1.fast5 | 1257 | AAACA

I want to know the coordinate is m6A modified or not.

Because in the ratio.x.tsv file some coordinates are missing which are present in genome_abandance.x.bed file, I search it in your readme file but I can't find so I just ask you. Thanks in advance

gaoyubang commented 2 years ago

The ratio.x.tsv is the final output, we fillter the genome_abandance.x.bed and then generate ratio.x.tsv.

aman21392 commented 2 years ago

ok, thanks but if the ratio.x.tsv file is also like genome_abandance.x.bed file then it's easy to extract all coordinates with gene name. I want to intersect the coordinates but first I have to arrange the coordinates only one in each row. So is possible to make a file like genome_abandance.x.bed file. Thanks in advance

gaoyubang commented 2 years ago

You can fillter the genome_abandance.x.bed through ratio.x.tsv file.

aman21392 commented 2 years ago

can you please tell me how because they are two different types of file one file have only 6 columns and a ratio.x.tsv file has multiple columns. I just try the grep command but it didn't help. Thanks in advance

gaoyubang commented 2 years ago

wget https://raw.githubusercontent.com/gaoyubang/nanom6A/main/fillter_output.py python fillter_output.py result_final/ratio.x.tsv result_final/genome_abandance.x.bed The output result_final/genome_abandance.x.bed.filler.bed is the filltered output.

aman21392 commented 2 years ago

thank you very much for sharing this python script. It gives me the file which I want.