Comments (7)
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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Related Issues (20)
- How to get result of miCLIP? HOT 1
- Eventalign.txt file is too large HOT 6
- Difference between mod_ratio and probability_modified HOT 1
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- Reproducing Fig 2d,e; request for transcriptome2genome.py for dummies HOT 2
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- Modification of n_read_per_site HOT 3
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- question about species HOT 1
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- Arabidopsis m6anet model for RNA004 HOT 2
- Inference JSONDecoderError HOT 2
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