a-slide / NanoCount

EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2

https://a-slide.github.io/NanoCount/

a-slide/NanoCount Issues

Latest version is not on pypi, please publish
Updated a month ago1
NanoCount MIN_QUERY_FRACTION_ALIGNED parameter default setting
Updated a month ago1
Raw counts for downstream analysis
Closed a year ago2
nanocount for two condition
Closed 2 years ago7
Can I directly map reads directly to genes instead of transcripts to estimate the expression in gene level?
Closed 4 months ago1
How do NanoCount deal with reads with multiple alignments?
Closed 6 months ago3
Nanocount vs Flair
Closed a year ago3
ERROR: No valid secondary alignments found in bam file. Were the reads aligned with minimap `-p 0 -N 10` options ?
Closed 8 months ago1
How can I obtain the raw file containing reads assigned to isoforms?
Closed 8 months ago1
Normalised the reads count
Closed 9 months ago1
Est_count doesn't match records
Closed a year ago3
Identical tpm values for different transcripts
Closed a year ago2
High % of reads lost due to discarded negative strand and invalid 3' end.
Closed a year ago2
transcript_name is chromosome name instead of gene name
Closed a year ago1
Transcript expression level to Gene expression
Closed a year ago
High % of sequences lost in discarded negative strand alignments
Closed a year ago3
Too many reads are discarded
Closed a year ago1
How to deal with multiple ensemble IDs mapping to one gene symbol in a RNA-Seq dataset
Closed a year ago1
Adding option for cDNA reads
Closed 2 years ago3
Why NanoCount needs sorted alignments?
Closed 2 years ago2
-N 100 hinder NanoCount accuracy?
Closed 2 years ago2
alignmnet using sequin reference
Closed 2 years ago1
nanocount fast5 files
Closed 2 years ago1
about data of nanocount paper
Closed 2 years ago1
Different options when using minimap
Closed 2 years ago2
Minimum number of ONT reads per sample
Closed 2 years ago1
Setting -3 to -1 to deactivate fails
Closed 3 years ago2
No valid secondary alignment found in bam file
Closed 4 years ago1
Using with custom filtered alignments
Closed 4 years ago5
ZeroDivisionError: division by zero
Closed 4 years ago6
Write a usage notebook instead of having usage in the README
Closed 4 years ago
TPM values do not sum up to 1 million
Closed 4 years ago1
Extract all references and length
Closed 4 years ago
Question about normalisation
Closed 4 years ago2