Closed BioinfoHub-PeiQinNg closed 2 years ago
Your _nreads column is also empty which is probably the initial problem.
Could you show the head
of m6anet-dataprep
outputs:
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.
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} \
Thank you @Stakaitis for helping to respond. @BioinfoHub-PeiQinNg your nanopolish eventalign is missing --signal-index argument which tells m6Anet the segment length information
I see. I will give it another go. Thank you so much!
hi @BioinfoHub-PeiQinNg, how is it working with you? Are you able to get the results now?
Hi @chrishendra93 , sorry for the late reply. I manage to get it running now! Thank you so much for your help! Cheers ^^
Hi there,
I have tried running
m6anet run-inference
to predict m6A modifications on my nanopore data.This was done based on the quick start tutorial https://m6anet.readthedocs.io/en/latest/quickstart.html
However, when I have a look at the output file, instead of indicating a
0
or a1
as shown in the examples, mine turns out to be a blank column.For your reference I have attached a snippet of my output file:
transcript_id, transcript_position, n_reads, probability_modified, kmer 2L, 74989, 31, ,TGACT 2L, 75008, 32, ,AAACT 2L, 75100, 33, ,TAACA 2L, 75106, 31, ,TGACT 2L, 75151, 35, ,AAACT
If you can provide me some guidance with this that will be great. Thank you!