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# My favourite sushi
### Hoso Maki / Roll
* #119
* #120
* #123 - prawn, crab, salmon, spring onion
* Soho - crab, avocado, prawn, smoked salmon
* Seattle - cucumber, avocado, raw salmon, sm…
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I have human RNA-Seq dataset it has two different barcodes in the different folder. I aligned with that command
minimap2 -ax splice -uf -k14 ref.fa direct-rna.fq > aln.sam
I try to quantify and coun…
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A common use case for transcriptomics doesn't involve de novo assembly, but rather just quantification or (perhaps) annotation + quantification, for semi-model organisms like dog and cat which have go…
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Hi. Dr. Thomas Bradley,
I found your paper, FilTar: using RNA-Seq data to improve microRNA target prediction accuracy in animals, and your program really fit into my project.
On the first attemp…
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Hi all,
First of all, thank you for making such a great tool. I have a question regarding the differences in mapping rates when using different indexing methods in salmon. I have a paired end RNA-…
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Some participants sometimes don't create the `salmon_outputs` directory from the first session and this then breaks the [`saveRDS` in Data Exploration section](https://github.com/bioinformatics-core-s…
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### Context
Salmon assumes that the reads you give it are in a random order -- see the first **Note** [here](https://salmon.readthedocs.io/en/latest/salmon.html#using-salmon) in the Salmon docs…
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The 10x Fixed RNA Profiling kit has some benefits with respect to the standard kit. For example, cells can be stored before library prep, there is a gene targeting mechanism based on specific targete…
rob-p updated
2 months ago
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Hi Brian,
I have produced the volcano plots with my replicates X3 however, it has created these files
salmon.gene.counts.matrix.P1_vs_P2.edgeR.count_matrix
salmon.gene.counts.matrix.P1_…
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k = 21 ~= genus
k = 31 ~= species
k = 51 ~= strain
If we do best RNA-seq sample reference matching at k = 31, check if decreasing salmon k-mer size (if it's parameterized) increases mapping rate…