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nloyfer / wgbs_tools

tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies
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BAM2PAT nanopore #88

Closed Sepideh89 closed 1 week ago

Sepideh89 commented 1 week ago

Dear WGBS Team,

I ran this command: wgbstools bam2pat -np test.bam this is a nanopore unaligned bamfile. seems to me wgbstools still trying to catch the chr name (while its an unaligned bam file, doesn't have chr name,etc.), however -np flag is active. this is the output of that command, could you please let me know if there is anything wrong running that command?

###################################################### Failed retrieving valid chromosome names. Perhaps you are using a wrong genome reference. Try running: wgbstools set_default_ref -ls Invalid input argument Failed

########################################################## Appreciate it in advance Sep.

yonniejon commented 1 week ago

Hi Sep, the input to wgbstools is required to be aligned. The pat format is only defined on aligned data as it requires reference CpG site genomic positions.

Sepideh89 commented 1 week ago

Thank you for your guidance.

yonniejon commented 1 week ago

Is this for targeted sequencing? If yes, then a common solution is to create a reference genome using your target sequence (or your target sequence with some padding on the sides).

Sepideh89 commented 1 week ago

This is Whole Genome Sequencing data. What's your advice regarding that?

yonniejon commented 1 week ago

For whole genome sequencing I recommend aligning the data to a reference genome 😅 . Why not align it?

Sepideh89 commented 1 week ago

I don't think I have any other choice. 💯 Thank you!