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Hi developers!!
## Background
I am using Alevin to align the P.Falciparum single cell dataset. For this sample we got a total of 27% of reads aligning using CellRanger and I am expecting this number…
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There are situations where users want to change e.g. featureCounts options, or bring in already prepared read alignments (sorted BAMs) so in such cases it would benefit to have the option to skip the …
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RNA-Skim: a rapid method for RNA-Seq quantification at transcript level
http://bioinformatics.oxfordjournals.org/content/30/12/i283.full.pdf+html
Li HD, Menon R, Omenn GS, Guan Y. (2014) The emerging…
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Thank you for this helpful software.
I'm looking to look at the raw fastq reads for transcripts that came up as differentially expressed after quantification with Salmon. Is there a good way to li…
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One problem I often run Into is that the sequence quality of the reads are problematic so I would like to trim the files based on sequence quality before. When I do that, fx with [trimmomatic](http://…
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Hi Sam, its me again here.
Tried running the program again with TCGA samples, but unfortunately immediately ran into this new error.
When running the preprocessing, I realise that the tag direc…
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This is a continuation of a discussion started in #68. I am moving it here because it appears that my problem has a different cause from the what appears to be the cause in #68.
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* sRNA analysis pipeline version: 3.6.2
* Python version: 3.10.9
* Operating System: Windows
### Description
I have used RNAlysis before, I was just trying to use the kallisto gene quantificat…
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Hi,
We've been trying out rpvg on a crop plant and it looks very promising!
I have a question regarding inferring haplotype probability when read counts are 0.
Index was built using autoindex and q…
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Hi,
I would like to use RSEM to quantify some nuclei RNA-seq data.
STAR version=2.7.9a
RSEM version=1.3.3
The code I used are:
###generate rsem reference
#use GRCm38_102 genome and gtf …