speed up rule save_counts (bottleneck) about scrnaseq_processing_seurat HOT 1 CLOSED

not the same! differences

• quotes -> fine/fixed
• column names differ '-' vs '.' -> check in metadata -> has to match for downstream tasks -> in metadata its '-'
• last row -> no gene name but rownumber?! -> fixed

new comparison
diff --brief <(tail -n +2 NORMALIZED_RNA.csv | cut -d, -f2-) <(tail -n +2 NORMALIZED_RNA_original.csv | cut -d, -f2-)
Files /dev/fd/63 and /dev/fd/62 differ

compare with brief diff
diff --brief NORMALIZED_RNA_original.csv NORMALIZED_RNA.csv

head -n 1 NORMALIZED_RNA.csv | cut -c 1-100
"",EMICROP_A_AAACCTGAGAATAGGG-1,EMICROP_A_AAACCTGAGACAATAC-1,EMICROP_A_AAACCTGAGACGACGT-1,EMICROP_A_

head -n 1 NORMALIZED_RNA_original.csv | cut -c 1-100
"","EMICROP_A_AAACCTGAGAATAGGG.1","EMICROP_A_AAACCTGAGACAATAC.1","EMICROP_A_AAACCTGAGACGACGT.1","EMI

tail -n 1 NORMALIZED_RNA.csv | cut -c 1-100
"28441",0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,

tail -n 1 NORMALIZED_RNA_original.csv | cut -c 1-100
"AC007325.4",0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

from scrnaseq_processing_seurat.