a-slide NanoCount issues

a-slide / NanoCount

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

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

MIT License

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issues

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Can I directly map reads directly to genes instead of transcripts to estimate the expression in gene level?

#37 kerenzhou062 closed 3 weeks ago
1
How do NanoCount deal with reads with multiple alignments?

#36 kerenzhou062 closed 3 months ago
3
ERROR: No valid secondary alignments found in bam file. Were the reads aligned with minimap `-p 0 -N 10` options ?

#35 lborcard closed 5 months ago
1
How can I obtain the raw file containing reads assigned to isoforms?

#34 zhenyu7500 closed 5 months ago
1
Normalised the reads count

#33 M-Chi-1 closed 6 months ago
1
Est_count doesn't match records

#32 KunFang93 closed 9 months ago
3
transcript_name is chromosome name instead of gene name

#31 KunFang93 closed 10 months ago
1
High % of reads lost due to discarded negative strand and invalid 3' end.

#30 NStrowbridge closed 9 months ago
2
Identical tpm values for different transcripts

#29 chloebonenfant closed 9 months ago
2
Nanocount vs Flair

#28 sagnikbanerjee15 closed 10 months ago
3
Transcript expression level to Gene expression

#27 vetmohit89 closed 10 months ago
0
Too many reads are discarded

#26 vetmohit89 closed 11 months ago
1
How to deal with multiple ensemble IDs mapping to one gene symbol in a RNA-Seq dataset

#25 vetmohit89 closed 1 year ago
1
Raw counts for downstream analysis

#24 lubitelpospat closed 1 year ago
1
High % of sequences lost in discarded negative strand alignments

#23 NStrowbridge closed 11 months ago
3
Retain neg strand

#22 josiegleeson closed 1 year ago
0
Update README.md

#21 josiegleeson closed 1 year ago
0
Why NanoCount needs sorted alignments?

#20 callumparr closed 1 year ago
2
-N 100 hinder NanoCount accuracy?

#19 callumparr closed 1 year ago
2
alignmnet using sequin reference

#18 rezarahman12 closed 1 year ago
1
nanocount fast5 files

#17 rezarahman12 closed 1 year ago
1
about data of nanocount paper

#16 rezarahman12 closed 1 year ago
1
nanocount for two condition

#15 rezarahman12 closed 1 year ago
7
Different options when using minimap

#14 Tomcxf closed 1 year ago
2
Minimum number of ONT reads per sample

#13 ms-gx closed 1 year ago
1
Adding option for cDNA reads

#12 camillaugolini-iit closed 1 year ago
3
Setting -3 to -1 to deactivate fails

#11 josiegleeson closed 2 years ago
2
No valid secondary alignment found in bam file

#10 jhwan1203 closed 3 years ago
1
Dev

#9 a-slide closed 4 years ago
0
Using with custom filtered alignments

#8 josiegleeson closed 4 years ago
5
Dev

#7 a-slide closed 4 years ago
0
Dev

#6 a-slide closed 4 years ago
0
ZeroDivisionError: division by zero

#5 callumparr closed 4 years ago
6
Question about normalisation

#4 tleonardi closed 4 years ago
2
TPM values do not sum up to 1 million

#3 lpryszcz closed 4 years ago
1
Write a usage notebook instead of having usage in the README

#2 a-slide closed 4 years ago
0
Extract all references and length

#1 a-slide closed 4 years ago
0