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Hi Shuangshuang,
Considering a gene can produce multiple transcripts, is there a method to obtain a transcript counting matrix instead of a gene-based one during data preprocessing?
Thank you!
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Dear Team,
I run Whippet on my paired-end, unstranded, polyA+ RNA-seq dataset. The dataset is of 75bp length (all reads in all samples have this length) and performed in triplicates per condition (…
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hi!
How to produce a PAS annotation file? My research species is fish, if i have a PAS annotation file of fish, could i use this software?
THANK YOU1
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When I process the raw fastq file from the test files, it always print "Error in data process module". I don't know what's wrong with my code.
Is the -index parameter wrong?
Here is my code. T…
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Hello, before writing further, I want to say that I have read through previous related open/closed issues but could not find a suitable answer.
The problem: rather different mapping rates depending…
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So I had problems running nanopolish and decided to build it from the docker image provided at https://quay.io/repository/biocontainers/nanopolish?tab=tags&tag= just to finnaly get it to work. Running…
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Dear dev team,
I want to generate a meta-assembly using samples from multiple datasets, which is a mixture of different seq protocol (polya or total rna) and different strandness (unstranded or fr-…
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Hello, i made a few years ago a solution for polya with rotations and reflections that should be sub-quadratic order on O(n*log^2(n)) if you'd like i could find my code and submit it, it's on c++ thou…
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Hey! Thanks for the great program.
There were two things that would, in my eyes, really round out the utility of this tool.
1) Removal of PolyA/T tails. Only a subset of my reads still contain a…
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Hello,
Could you add an option to trimming polyT from the 5'? I think it is useful for filtering polyT stretches coming from polyA tails in unstranded RNA-seq data.
Thanks,
Haibo