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DeepTools.sh
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DeepTools.sh
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#################################### install deeptools ###################################
# fasta file can be converted to 2bit using the UCSC programm called faToTwoBit
# http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/faToTwoBit
module load python/3.7.3
source ~/mypython3env/bin/activate
pip install deeptools
export PATH=/srv/scratch/z5039045/Softwares/faToTwoBit:$PATH
computeGCBias -b file.bam --effectiveGenomeSize 2150570000 -g mm9.2bit -l 200 --GCbiasFrequenciesFile freq.txt
###################################### run deeptools #####################################
perl /srv/scratch/z5039045/Scripts/get_fasta_stats.pl -T FP.fna
# Number of Contigs=1, Total bp=2166381, Shortest=2166381, Longest=2166381, Average length=2166381.0, Average GC%=38.9%, Non-ACGT bases=0
module load python/3.7.3
source ~/mypython3env/bin/activate
export PATH=/srv/scratch/z5039045/Softwares/faToTwoBit:$PATH
cd /srv/scratch/z5039045/MarkerMAG_wd/MBARC26/map_to_ref_gnm_sep
faToTwoBit FP.fna FP.2bit
computeGCBias -b FP_report_best_mis0_sorted.bam --effectiveGenomeSize 2166381 -g FP.2bit -l 200 -p 12 --GCbiasFrequenciesFile FP_GC_bias_freq.txt
computeGCBias -b FP_report_best_mis0_sorted.bam --effectiveGenomeSize 2166381 -g FP.2bit -l 200 -p 12 --GCbiasFrequenciesFile FP_GC_bias_freq.txt --biasPlot FP_GC_bias_freq.pdf --plotFileFormat pdf
correctGCBias -b FP_report_best_mis0_sorted.bam --effectiveGenomeSize 2166381 -g FP.2bit --GCbiasFrequenciesFile FP_GC_bias_freq.txt -o gc_corrected.bam
######################################## Illumina ########################################
# GC Bias Report
# https://support.illumina.com/content/dam/illumina-support/help/Illumina_DRAGEN_Bio_IT_Platform_v3_7_1000000141465/Content/SW/Informatics/Dragen/GCBiasReport_fDG.htm
# GC Bias Correction
# https://support.illumina.com/content/dam/illumina-support/help/Illumina_DRAGEN_Bio_IT_Platform_v3_7_1000000141465/Content/SW/Informatics/Dragen/BiasCorrections_fDG_dtSW.htm
dragen -b FP_report_best_mis0_sorted.bam -r FP.fna --gc-metrics-enable=true