probability_modified column is empty about m6anet HOT 7 CLOSED

Your n_reads column is also empty which is probably the initial problem.
Could you show the head of m6anet-dataprep outputs:

• data.log
• data.readcount
• eventalign.index
• data.index

from m6anet.

Hi there,
Thank you for getting back to me.

These are what the few output head of m6anet-dataprep looks like

• head data.log
  2L: Data preparation ... Done.
  2R: Data preparation ... Done.
  3L: Data preparation ... Done.
  3R: Data preparation ... Done.
  4: Data preparation ... Done.
  X: Data preparation ... Done.
  Y: Data preparation ... Done.
  dmel_mitochondrion_genome: Data preparation ... Done.
  Unmapped_Scaffold_8: Data preparation ... Done.
  3Cen_mapped_Scaffold_31: Data preparation ... Done.

• head data.readcount
  transcript_id,transcript_position,n_reads
  2L,49675,1
  2L,51533,1
  2L,51692,1
  2L,51748,1
  2L,51783,1
  2L,51792,1
  2L,51883,2
  2L,51927,1
  2L,52054,2

• eventalign.index
  transcript_id,read_index,pos_start,pos_end
  2L,0,154,56988
  2L,1,56988,117016
  2L,2,117016,229586
  2L,3,229586,470294
  2L,5,470294,934066
  2L,6,934066,1334426
  2L,7,1334426,1873408
  2L,8,1873408,2155664
  2L,9,2155664,2304450

• head data.index
  transcript_id,transcript_position,start,end
  2L,49675,0,69
  2L,51533,69,138
  2L,51692,138,207
  2L,51748,207,276
  2L,51783,276,345
  2L,51792,345,414
  2L,51883,414,521
  2L,51927,521,590
  2L,52054,590,697

Thank you again for assisting me with this.

from m6anet.

I have also provided the command lines that I have used for nanopore eventalign and m6a-dataprep for your reference:

nanopolish eventalign \ --reads {input.fasta} \ --bam {input.bam} \ --genome {input.ref} \ --scale-events > {SAMPLE}-ref.eventalign.txt

m6anet-dataprep --eventalign {input.txt} \ --out_dir {output} \

from m6anet.

Thank you @Stakaitis for helping to respond. @BioinfoHub-PeiQinNg your nanopolish eventalign is missing --signal-index argument which tells m6Anet the segment length information

from m6anet.

I see. I will give it another go. Thank you so much!

from m6anet.

hi @BioinfoHub-PeiQinNg, how is it working with you? Are you able to get the results now?

from m6anet.

Hi @chrishendra93 , sorry for the late reply. I manage to get it running now! Thank you so much for your help! Cheers ^^

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