~/bak/doc/fleming/kafasla/DKlab/mr/rnaseq/README-processing.txt
~/.local/bin/cutadapt -j 16  -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTAT  -o wt01_R1_trm.fastq.gz -p wt01_R2_trm.fastq.gz    /mnt/max/b/genomics_facility/DKlab/mr/rnaseq/RNA_Seq/HI.1370.002.Index_10.wt01_R1.fastq.gz  /mnt/max/b/genomics_facility/DKlab/mr/rnaseq/RNA_Seq/HI.1370.002.Index_10.wt01_R2.fastq.gz
Total read pairs processed:       42154307
]0;~/bak/doc/fleming/kafasla/DKlab/mr/rnaseqreczko@max:~/bak/doc/fleming/kafasla/DKlab/mr/rnaseq$ grep "Total read pairs processed" *trm.log
KO01_R1_trm.log:Total read pairs processed:         47200988
KO02_R1_trm.log:Total read pairs processed:         59125771
KO21_R1_trm.log:Total read pairs processed:         57026220
KO22_R1_trm.log:Total read pairs processed:         56186681
KO61_R1_trm.log:Total read pairs processed:         53427409
KO62_R1_trm.log:Total read pairs processed:         63949215
KOIFN_1_R1_trm.log:Total read pairs processed:         58828408
KOIFN_2_R1_trm.log:Total read pairs processed:         51064246
KOIL4_1_R1_trm.log:Total read pairs processed:         59014199
KOIL4_2_R1_trm.log:Total read pairs processed:         60779853
wt02_R1_trm.log:Total read pairs processed:         43055164
wt21_R1_trm.log:Total read pairs processed:         39742554
wt22_R1_trm.log:Total read pairs processed:         46760661
wt61_R1_trm.log:Total read pairs processed:         45891803
wt62_R1_trm.log:Total read pairs processed:         44353854
wtIFN_1_R1_trm.log:Total read pairs processed:         45875430
wtIFN_2_R1_trm.log:Total read pairs processed:         60663417
wtIL4_1_R1_trm.log:Total read pairs processed:         54254443
wtIL4_2_R1_trm.log:Total read pairs processed:         41543001

]0;/data/images/proton/DKlab/mr/rnaseqreczko@max:/data/images/proton/DKlab/mr/rnaseq$ grep "Total written" *trm.log
KO01_R1_trm.log:Total written (filtered):  9387220832 bp (99.4%)
KO02_R1_trm.log:Total written (filtered):  11758362436 bp (99.4%)
KO21_R1_trm.log:Total written (filtered):  11347410203 bp (99.5%)
KO22_R1_trm.log:Total written (filtered):  11180041981 bp (99.5%)
KO61_R1_trm.log:Total written (filtered):  10630673572 bp (99.5%)
KO62_R1_trm.log:Total written (filtered):  12722317195 bp (99.5%)
KOIFN_1_R1_trm.log:Total written (filtered):  11720924138 bp (99.6%)
KOIFN_2_R1_trm.log:Total written (filtered):  10168835490 bp (99.6%)
KOIL4_1_R1_trm.log:Total written (filtered):  11735750465 bp (99.4%)
KOIL4_2_R1_trm.log:Total written (filtered):  12108317387 bp (99.6%)
wt02_R1_trm.log:Total written (filtered):  8567821554 bp (99.5%)
wt21_R1_trm.log:Total written (filtered):  7901614944 bp (99.4%)
wt22_R1_trm.log:Total written (filtered):  9297431922 bp (99.4%)
wt61_R1_trm.log:Total written (filtered):  9127749549 bp (99.4%)
wt62_R1_trm.log:Total written (filtered):  8827177513 bp (99.5%)
wtIFN_1_R1_trm.log:Total written (filtered):  9134338978 bp (99.6%)
wtIFN_2_R1_trm.log:Total written (filtered):  12074928496 bp (99.5%)
wtIL4_1_R1_trm.log:Total written (filtered):  10791460543 bp (99.5%)
wtIL4_2_R1_trm.log:Total written (filtered):  8265362366 bp (99.5%)

(/ (+ 99.4 99.4 99.5 99.5 99.5 99.5 99.6 99.6 99.4 99.6 99.5 99.4 99.4 99.4 99.5 99.6 99.5 99.5 99.5 ) 19.0)
99.48947368421054

(/ 168617228 4)
42154307

grep "Pairs written" *.log
KO01_R1_trm.log:Pairs written (passing filters):    47,200,988 (100.0%)
KO02_R1_trm.log:Pairs written (passing filters):    59,125,771 (100.0%)
KO21_R1_trm.log:Pairs written (passing filters):    57,026,220 (100.0%)
KO22_R1_trm.log:Pairs written (passing filters):    56,186,681 (100.0%)
KO61_R1_trm.log:Pairs written (passing filters):    53,427,409 (100.0%)
KO62_R1_trm.log:Pairs written (passing filters):    63,949,215 (100.0%)
KOIFN_1_R1_trm.log:Pairs written (passing filters):    58,828,408 (100.0%)
KOIFN_2_R1_trm.log:Pairs written (passing filters):    51,064,246 (100.0%)
KOIL4_1_R1_trm.log:Pairs written (passing filters):    59,014,199 (100.0%)
KOIL4_2_R1_trm.log:Pairs written (passing filters):    60,779,853 (100.0%)
wt02_R1_trm.log:Pairs written (passing filters):    43,055,164 (100.0%)
wt21_R1_trm.log:Pairs written (passing filters):    39,742,554 (100.0%)
wt22_R1_trm.log:Pairs written (passing filters):    46,760,661 (100.0%)
wt61_R1_trm.log:Pairs written (passing filters):    45,891,803 (100.0%)
wt62_R1_trm.log:Pairs written (passing filters):    44,353,854 (100.0%)
wtIFN_1_R1_trm.log:Pairs written (passing filters):    45,875,430 (100.0%)
wtIFN_2_R1_trm.log:Pairs written (passing filters):    60,663,417 (100.0%)
wtIL4_1_R1_trm.log:Pairs written (passing filters):    54,254,443 (100.0%)
wtIL4_2_R1_trm.log:Pairs written (passing filters):    41,543,001 (100.0%)