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### Ask away!
Hi! I have a quick question. I've read several post that people have their processes stuck specifically at stringtie step for large input, and I've encounter the same. Specifically, it …
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Hi,
My interest is "differenctial transcript usage".
**My question is:**
How could I obtain differential gene (not transcript) expression? Using (the formatted) iso_tpm file? Then I could analy…
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Hi,
I already have a reference transcript. How to quantify the existing reference transcripts and quantify the reference transcripts for each read sample
JXAUDZF
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I know I keep asking a bunch of questions that are probably specific for the pipeline we use, sorry if these are mostly irrelevant for others...
In our case, we use filtered and unfiltered abundanc…
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Hello dear Salmon developers,
First of all - thank you very much for your effort in supporting Oxford Nanopore reads! I've been Salmon for quantification of ONT sequencing experiments, and recently I…
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Hi,
Since eXpress is not being maintained and kallisto is among the state-of-the-art transcript quantification tools, can kallisto output (quantified on transcript.fa) being support by KMA? Thanks.
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Hello - thank you for engineering such a helpful tool.
I'm running through the tutorial and examining the file "gene_wise_quantifications_combined.tsv", which I understand contains genewise/transcr…
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In [rna-seq.tex](https://github.com/klmr/thesis/blob/master/rna-seq.tex) you have excellent discussion of various aspects of expression quantification. I think there are some missing pieces:
- Given t…
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Hello,
I am simulating reads in transcriptome mode. For this purpose, I have created an expression profile in the specified format. The read counts generated per transcript are different from what…
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HI,gpertea.
Histat2 can add XS tag for all read alignments,I have a stranded library (fr-firststrand) data, I use STAR to mapping genome and set options --outSAMstrandField intronMotif which can add …