Commit 60a50030 authored by Lena Hersemann's avatar Lena Hersemann

Merge remote-tracking branch 'origin/master'

parents 00632614 c92d7066
......@@ -53,7 +53,7 @@ dge_fastqc $(ls *fastq.gz) &
mcdir ${PRJ_DATA}/lanereps_pooled
echo '
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.36/R/core_commons.R")
devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v1.42/R/core_commons.R")
sheetFile <- "../originals/natalied-FC_SN678_338-2015-5-12.xls"
......@@ -132,7 +132,7 @@ mcdir ${PRJ_DATA}/dge_analysis
#
rend.R -e ${NGS_TOOLS}/dge_workflow/featcounts_deseq_mf.R ../alignments/star_counts_matrix.txt 2>&1 | tee featcounts_deseq.log
rend.R -e ${NGS_TOOLS}/dge_workflow/featcounts_deseq_mf.R ../alignments/star_counts_matrix.txt ${PRJ_DATA}/lanereps_pooled/basic_design.txt 2>&1 | tee featcounts_deseq.log
#rend.R -e ${NGS_TOOLS}/dge_workflow/featcounts_deseq_mf.R --design 'batch+sample' --pcutoff 0.01 --contrasts ../contrasts_wt.txt ../qseq.counts.txt ../qseq.design_matrix.txt 2>&1 | tee featcounts_deseq_mf.log
......
......@@ -229,6 +229,10 @@ wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/NCBI/GRCh38/Homo
tar xvf Homo_sapiens_NCBI_GRCh38.tar.gz
## notes
# GRCh37 (hg19)
# GRCh38 (hg38)
......@@ -310,3 +314,6 @@ cmake ..
make
## or fetch existing build
wget https://github.com/pachterlab/kallisto/releases/download/v0.43.1/kallisto_linux-v0.43.1.tar.gz
tar xvf kallisto_linux-v0.43.1.tar.gz
\ No newline at end of file
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment