snakemake-rna-seq issueshttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues2023-12-21T13:23:25+01:00https://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/24more stringent pre-filtering on low expressed genes2023-12-21T13:23:25+01:00Aurélien Ginolhacmore stringent pre-filtering on low expressed geneshttps://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
``` r
smallestGroupSize <- 3
keep <- rowSums(counts(dds) >= 10) >= smallestGroupSize
dds <- dds[keep,]
```https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
``` r
smallestGroupSize <- 3
keep <- rowSums(counts(dds) >= 10) >= smallestGroupSize
dds <- dds[keep,]
```Aurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/23min quality, 30 too much?2023-11-08T16:31:52+01:00Aurélien Ginolhacmin quality, 30 too much?https://support.bioconductor.org/p/117597/https://support.bioconductor.org/p/117597/Aurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/22Add QoRTS2023-11-08T13:32:34+01:00Aurélien GinolhacAdd QoRTShttp://hartleys.github.io/QoRTs/doc/QoRTs-vignette.pdfhttp://hartleys.github.io/QoRTs/doc/QoRTs-vignette.pdfAurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/19implement the nice updates in v2 of the original template2023-05-02T10:40:40+02:00Aurélien Ginolhacimplement the nice updates in v2 of the original templateespically the deseq2 upgrade
https://github.com/snakemake-workflows/rna-seq-star-deseq2/releases/tag/v2.0.0espically the deseq2 upgrade
https://github.com/snakemake-workflows/rna-seq-star-deseq2/releases/tag/v2.0.0Aurélien GinolhacAurélien Ginolhachttps://git-r3lab.uni.lu/aurelien.ginolhac/snakemake-rna-seq/-/issues/7cannot trim with more than one adapter2021-06-11T14:36:31+02:00Aurélien Ginolhaccannot trim with more than one adapter`AdapterRemoval` can use a file for trim with > 1 adapter.
Filipe found a nice solution [in his wrapper](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/adapterremoval.html)
quick and dirty solution in `/work/projects/hncf...`AdapterRemoval` can use a file for trim with > 1 adapter.
Filipe found a nice solution [in his wrapper](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/adapterremoval.html)
quick and dirty solution in `/work/projects/hncfp` missing assertion files `adapters.txt` existAurélien GinolhacAurélien Ginolhac