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Hi,
I have a question about the true strand of assembled sequences based on strand-specific reads. Are they all the true mRNA sequences or might be their reverse complements? In other words, will t…
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Dear Salmon team,
We have previously been using salmon 0.8.1 for our RNA sequencing analysis pipeline and wanted to upgrade to the latest version (1.3.0). Upon comparing the quant.sf output from sa…
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Dear Martin,
Thanks for developing this wonderful software for TE expression quantification. I have a question regarding the de novo transcriptome. For non-model organism, we could perform a de nov…
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In our mouse cDNA data, we hypothesise that mt-Atp6 and mt-Atp8 are encoded together on the mouse mitochondrial genome as a single polycistronic unit, which is demonstrated by observing co-expression …
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[RNA-Seq read representation of the assembly](https://github.com/trinityrnaseq/trinityrnaseq/wiki/RNA-Seq-Read-Representation-by-Trinity-Assembly)
I am following the steps described in the tutorial…
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**Copy and paste the exact command you tried to run**
```
flair collapse -q merged_alignments.bed --genome hg38_no_alt.fa --reads merged.fastq --gtf Homo_sapiens.GRCh38.100.remapped.gtf …
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When using the -z option to obtain a SAM file and using that same SAM file as an input for a quantification, the following error is thrown:
```
Version Info: This is the most recent version of s…
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I get the following error when running prepDE.py on stringtie estimate output:
```
Traceback (most recent call last):
File "./prepDE.py", line 255, in
geneDict.setdefault(geneIDs[i],{}) #…
ms-gx updated
3 months ago
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Hi, thank you for providing such a wonderful resources to the community. I am trying to analyze the data to compare performance of multiple quantification program. To do that, I downloaded cDNA PCR se…
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I am working with Salmon in mapping-based mode to perform differential expression.
I am interested to understand which reads Salmon uses to produce counts, so I added --writeMappings and I checked th…