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Commit a1d529e3 authored by Christophe  BECAVIN's avatar Christophe BECAVIN
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Update README.txt

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......@@ -31,7 +31,7 @@ INSTALL first all dependencies: See INSTALL.txt
Run on every dataset:
WARNING - Steps 3 to 7 are run separately for each dataset
WARNING - They might take a ot of time to perform, so they can be parallelized on a cluster
WARNING - They might take a lot of time to perform, so they can be parallelized on a cluster
3 - Trimming, mapping, BAM file filtering and quality control
4 - Calculate SeqDepth for peak detection techniques
5 - HTSeq - Count number of reads per genes
......@@ -42,11 +42,11 @@ WARNING - They might take a ot of time to perform, so they can be parallelized o
Run only one time per project_name
8 - MultiQC for quality control
9 - finalize peak detection by filtering out "bad" peaks
10 - (Optionnal) Annotate all peaks from all different techniques
10 - (Optional) Annotate all peaks from all different techniques
11 - Regroup peaks from all the detection techniques, annotate them, find overlap position with genes and referent MeRIP-Seq, CLIPSeq and TREW
Run on every dataset:
12 - HTSeq - Count number of reads in each methylation sites detected
12 - HTSeq - Count number of reads in each methylation site detected
13 - Perform differential methylation sites analysis in R
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