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Commit 5482e034 authored by Rachel  LEGENDRE's avatar Rachel LEGENDRE
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add some comment in readme - new release comment

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......@@ -28,7 +28,7 @@ RNAflow is a snakemake pipeline dedicated to standard transcriptomic analysis [@
Be careful, RNAflow was mainly developped to run on the HPC of Institut Pasteur, and not on other HPC.
<img src="images/rulegraph.svg" width="700">
<img src="images/rulegraph.svg" width="1000">
## How to install RNAflow ?
......@@ -177,6 +177,9 @@ star_mapping:
```
> Junctions could be added by sample or from all samples to second pass. For experiments with more than 30 samples, choose by-sample instead of all-samples (to avoid RAM issue)
- Counting with Salmon (EM algorithm)
```
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......@@ -7,6 +7,20 @@
## Releases
31 Dec 2022:
- Optimize exon quantification is now available
Updates:
- Add salmon for quantification for eukaryotic genomes (https://doi.org/10.1371/journal.pone.0141910, https://doi.org/10.12688/f1000research.7563.2, https://doi.org/10.1016/j.csbj.2020.06.014)
- Mapping now starts from cleaned files (without rRNA) when sortmeRNA is set to yes
- Add IGV session from bigwig files
- Add fastq_screen
- genomeSAindexNbases and genomeChrBinNbits are automatically computed as desscribed in STAR manual
- connect output directory analysis
20 Nov 2021:
- Initial pipeline tested on Maestro and NNCR
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