diff --git a/2024/ebaiin1/chip-seq/hands-on/hands-on.Rmd b/2024/ebaiin1/chip-seq/hands-on/hands-on.Rmd index e0e875e..77679b3 100644 --- a/2024/ebaiin1/chip-seq/hands-on/hands-on.Rmd +++ b/2024/ebaiin1/chip-seq/hands-on/hands-on.Rmd @@ -152,7 +152,7 @@ Your directory structure should be like this ``` 3. Get FastQC available in your environment ```{bash eval=FALSE} -module load fastqc/0.12.1 +module load fastqc/0.11.9 ``` 4. Check the help page of the program to see its usage and parameters. @@ -274,7 +274,6 @@ Your directory structure should be like this: ```{bash eval=FALSE} ## Run alignment ## Tip: first type bowtie command line then add quotes around and prefix it with "sbatch --cpus 10 --wrap=" -module load formation/2421 sbatch -p fast -o FNR_IP_ChIP-seq_Anaerobic_A.mapping.out --cpus-per-task 10 --wrap="bowtie2 -p 10 --mm -3 1 -x ../index/Escherichia_coli_K12 -U ../../data/FNR_IP_ChIP-seq_Anaerobic_A.fastq.gz -S FNR_IP_ChIP-seq_Anaerobic_A.sam" ``` diff --git a/2024/ebaiin1/chip-seq/hands-on/hands-on.html b/2024/ebaiin1/chip-seq/hands-on/hands-on.html index c1e3314..b32aa76 100644 --- a/2024/ebaiin1/chip-seq/hands-on/hands-on.html +++ b/2024/ebaiin1/chip-seq/hands-on/hands-on.html @@ -1706,7 +1706,7 @@

4.1 - Generating the
  1. Get FastQC available in your environment
-
module load fastqc/0.12.1
+
module load fastqc/0.11.9
  1. Check the help page of the program to see its usage and parameters.
    2. @@ -1867,7 +1867,6 @@

    5.4 - Mapping the 
    ## Run alignment
 ## Tip: first type bowtie command line then add quotes around and prefix it with "sbatch --cpus 10 --wrap="
-module load formation/2421
 
 sbatch -p fast -o FNR_IP_ChIP-seq_Anaerobic_A.mapping.out --cpus-per-task 10 --wrap="bowtie2 -p 10 --mm -3 1 -x ../index/Escherichia_coli_K12 -U ../../data/FNR_IP_ChIP-seq_Anaerobic_A.fastq.gz -S FNR_IP_ChIP-seq_Anaerobic_A.sam"

    This should take few minutes as we work with a small genome. For the @@ -2797,8 +2796,8 @@

    12.2.5 - How does the # compute the density of peaks within the promoter regions tagMatrix = getTagMatrix(peaks.limb, windows=promoter) -
    ## >> preparing start_site regions by gene... 2024-11-19 09:52:26
-## >> preparing tag matrix...  2024-11-19 09:52:26
    +
    ## >> preparing start_site regions by gene... 2024-11-19 15:26:10
+## >> preparing tag matrix...  2024-11-19 15:26:10
    # plot the density
 tagHeatmap(tagMatrix, palette = "RdYlBu")

    @@ -2813,32 +2812,32 @@

    12.3 - Functional peak files with the annotation file of the mouse genome. This function returns a complex object which contains all this information.

    peakAnno.forebrain = annotatePeak(peaks.forebrain, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Mm.eg.db")
    -
    ## >> preparing features information...      2024-11-19 09:52:47 
-## >> identifying nearest features...        2024-11-19 09:52:47 
-## >> calculating distance from peak to TSS...   2024-11-19 09:52:47 
-## >> assigning genomic annotation...        2024-11-19 09:52:47 
-## >> adding gene annotation...          2024-11-19 09:52:52
    +
    ## >> preparing features information...      2024-11-19 15:26:31 
+## >> identifying nearest features...        2024-11-19 15:26:31 
+## >> calculating distance from peak to TSS...   2024-11-19 15:26:31 
+## >> assigning genomic annotation...        2024-11-19 15:26:31 
+## >> adding gene annotation...          2024-11-19 15:26:35
    ## 'select()' returned 1:many mapping between keys and columns
    -
    ## >> assigning chromosome lengths           2024-11-19 09:52:52 
-## >> done...                    2024-11-19 09:52:52
    +
    ## >> assigning chromosome lengths           2024-11-19 15:26:35 
+## >> done...                    2024-11-19 15:26:35
    peakAnno.midbrain = annotatePeak(peaks.midbrain, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Mm.eg.db")
    -
    ## >> preparing features information...      2024-11-19 09:52:52 
-## >> identifying nearest features...        2024-11-19 09:52:52 
-## >> calculating distance from peak to TSS...   2024-11-19 09:52:52 
-## >> assigning genomic annotation...        2024-11-19 09:52:52 
-## >> adding gene annotation...          2024-11-19 09:52:52
    +
    ## >> preparing features information...      2024-11-19 15:26:35 
+## >> identifying nearest features...        2024-11-19 15:26:35 
+## >> calculating distance from peak to TSS...   2024-11-19 15:26:35 
+## >> assigning genomic annotation...        2024-11-19 15:26:35 
+## >> adding gene annotation...          2024-11-19 15:26:36
    ## 'select()' returned 1:1 mapping between keys and columns
    -
    ## >> assigning chromosome lengths           2024-11-19 09:52:52 
-## >> done...                    2024-11-19 09:52:52
    +
    ## >> assigning chromosome lengths           2024-11-19 15:26:36 
+## >> done...                    2024-11-19 15:26:36
    peakAnno.limb = annotatePeak(peaks.limb, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Mm.eg.db")
    -
    ## >> preparing features information...      2024-11-19 09:52:52 
-## >> identifying nearest features...        2024-11-19 09:52:52 
-## >> calculating distance from peak to TSS...   2024-11-19 09:52:52 
-## >> assigning genomic annotation...        2024-11-19 09:52:52 
-## >> adding gene annotation...          2024-11-19 09:52:53
    +
    ## >> preparing features information...      2024-11-19 15:26:36 
+## >> identifying nearest features...        2024-11-19 15:26:36 
+## >> calculating distance from peak to TSS...   2024-11-19 15:26:36 
+## >> assigning genomic annotation...        2024-11-19 15:26:36 
+## >> adding gene annotation...          2024-11-19 15:26:37
    ## 'select()' returned 1:many mapping between keys and columns
    -
    ## >> assigning chromosome lengths           2024-11-19 09:52:53 
-## >> done...                    2024-11-19 09:52:53
    +
    ## >> assigning chromosome lengths           2024-11-19 15:26:37 
+## >> done...                    2024-11-19 15:26:37

    12.3.1 - genomic localization