Salmon + Sea lice data analysis
STEP 1. Copied data from mox to ostrich desktop via rsync in a screen
on mox:
screen -S rsync.TRIM1st5bp
rsync /gscratch/srlab/strigg/data/Salmo_Calig/TRIM_1st5bp/*.gz strigg@ostrich.fish.washington.edu:~/Desktop/Salmo_Calig
STEP 2. moved data to Gannet
ostrich:TRIM_1st5bp strigg$ pwd
/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_1st5bp
mv ~/Desktop/TRIM_1st5bp/ .
STEP 3. run check sums
on Gannet:
/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_1st5bp md5 * > checksums.md5
on Mox:
cd /gscratch/srlab/strigg/data/Salmo_Calig/TRIM_1st5bp
md5sum *.gz > checksums.md5
- this got delayed because of node maintenance
STEP 4. run fastqc on ostrich - see 20190722_SalmonSeaLice_FASTQC_TRIM.ipynb section “#run fastqc on trimmed 1st 5bp + adapter trimmed reads”
STEP 5. copy fastqc output to emu
srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ scp -r strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_1st5bp/FASTQC .
Password:
16C_32psu_2_S2_L002_R1_001_trimmed.5bp_3prime 100% 304KB 304.2KB/s 00:00
16C_32psu_1_S1_L001_R1_001_trimmed.5bp_3prime 100% 321KB 321.4KB/s 00:00
16C_32psu_4_S4_L001_R1_001_trimmed.5bp_3prime 100% 308KB 308.0KB/s 00:00
8C_26psu_4_S12_L001_R1_001_trimmed.5bp_3prime 100% 421KB 420.6KB/s 00:00
16C_32psu_4_S4_L001_R2_001_trimmed.5bp_3prime 100% 420KB 420.5KB/s 00:00
16C_26psu_3_S15_L001_R2_001_trimmed.5bp_3prim 100% 424KB 423.9KB/s 00:00
8C_26psu_3_S11_L001_R1_001_trimmed.5bp_3prime 100% 306KB 306.5KB/s 00:00
8C_32psu_2_S6_L002_R2_001_trimmed.5bp_3prime_ 100% 308KB 307.6KB/s 00:00
16C_26psu_4_S16_L002_R1_001_trimmed.5bp_3prim 100% 423KB 422.9KB/s 00:00
8C_26psu_2_S10_L002_R1_001_trimmed.5bp_3prime 100% 422KB 421.8KB/s 00:00
16C_32psu_1_S1_L002_R1_001_trimmed.5bp_3prime 100% 327KB 326.6KB/s 00:00
8C_26psu_2_S10_L001_R2_001_trimmed.5bp_3prime 100% 420KB 420.4KB/s 00:00
Sealice_F1_S20_L001_R1_001_trimmed.5bp_3prime 100% 414KB 414.1KB/s 00:00
8C_32psu_1_S5_L002_R2_001_trimmed.5bp_3prime_ 100% 421KB 421.0KB/s 00:00
16C_32psu_4_S4_L001_R2_001_trimmed.5bp_3prime 100% 313KB 313.1KB/s 00:00
CTRL_8C_26psu_1_S17_L002_R2_001_trimmed.5bp_3 100% 312KB 312.3KB/s 00:00
8C_26psu_4_S12_L002_R2_001_trimmed.5bp_3prime 100% 317KB 316.5KB/s 00:00
16C_32psu_2_S2_L002_R1_001_trimmed.5bp_3prime 100% 419KB 418.6KB/s 00:00
8C_32psu_2_S6_L001_R2_001_trimmed.5bp_3prime_ 100% 419KB 418.8KB/s 00:00
16C_26psu_2_S14_L001_R1_001_trimmed.5bp_3prim 100% 420KB 419.7KB/s 00:00
8C_26psu_3_S11_L001_R1_001_trimmed.5bp_3prime 100% 418KB 418.4KB/s 00:01
8C_32psu_4_S8_L002_R1_001_trimmed.5bp_3prime_ 100% 421KB 420.6KB/s 00:00
16C_32psu_3_S3_L002_R2_001_trimmed.5bp_3prime 100% 318KB 318.5KB/s 00:00
CTRL_8C_26psu_1_S17_L002_R1_001_trimmed.5bp_3 100% 420KB 420.2KB/s 00:00
CTRL_16C_26psu_1_S19_L001_R1_001_trimmed.5bp_ 100% 309KB 308.7KB/s 00:00
8C_32psu_3_S7_L002_R2_001_trimmed.5bp_3prime_ 100% 322KB 322.1KB/s 00:00
16C_32psu_1_S1_L002_R2_001_trimmed.5bp_3prime 100% 423KB 422.8KB/s 00:00
16C_32psu_2_S2_L001_R2_001_trimmed.5bp_3prime 100% 313KB 313.2KB/s 00:00
8C_26psu_3_S11_L002_R1_001_trimmed.5bp_3prime 100% 308KB 307.6KB/s 00:00
8C_26psu_1_S9_L001_R1_001_trimmed.5bp_3prime_ 100% 307KB 306.7KB/s 00:00
16C_32psu_4_S4_L002_R2_001_trimmed.5bp_3prime 100% 430KB 429.9KB/s 00:00
16C_32psu_3_S3_L002_R2_001_trimmed.5bp_3prime 100% 421KB 421.1KB/s 00:00
16C_26psu_4_S16_L002_R1_001_trimmed.5bp_3prim 100% 310KB 309.5KB/s 00:00
16C_26psu_2_S14_L002_R2_001_trimmed.5bp_3prim 100% 319KB 318.9KB/s 00:00
16C_32psu_2_S2_L002_R2_001_trimmed.5bp_3prime 100% 424KB 423.9KB/s 00:00
16C_26psu_3_S15_L001_R1_001_trimmed.5bp_3prim 100% 425KB 425.0KB/s 00:00
8C_26psu_2_S10_L001_R1_001_trimmed.5bp_3prime 100% 420KB 420.4KB/s 00:00
16C_26psu_1_S13_L002_R2_001_trimmed.5bp_3prim 100% 314KB 314.2KB/s 00:00
16C_26psu_4_S16_L001_R2_001_trimmed.5bp_3prim 100% 309KB 308.6KB/s 00:00
16C_26psu_2_S14_L001_R2_001_trimmed.5bp_3prim 100% 418KB 418.4KB/s 00:00
16C_32psu_1_S1_L002_R2_001_trimmed.5bp_3prime 100% 317KB 317.0KB/s 00:00
8C_32psu_3_S7_L001_R1_001_trimmed.5bp_3prime_ 100% 306KB 305.5KB/s 00:00
16C_32psu_2_S2_L001_R2_001_trimmed.5bp_3prime 100% 421KB 421.1KB/s 00:00
CTRL_8C_26psu_2_S18_L001_R1_001_trimmed.5bp_3 100% 421KB 420.9KB/s 00:00
CTRL_8C_26psu_1_S17_L001_R2_001_trimmed.5bp_3 100% 313KB 313.4KB/s 00:01
Sealice_F1_S20_L002_R1_001_trimmed.5bp_3prime 100% 417KB 417.0KB/s 00:00
8C_32psu_3_S7_L002_R2_001_trimmed.5bp_3prime_ 100% 424KB 423.7KB/s 00:00
Sealice_F1_S20_L002_R2_001_trimmed.5bp_3prime 100% 312KB 311.6KB/s 00:00
Sealice_F2_S22_L002_R1_001_trimmed.5bp_3prime 100% 421KB 421.5KB/s 00:00
CTRL_8C_26psu_1_S17_L001_R1_001_trimmed.5bp_3 100% 309KB 309.2KB/s 00:00
8C_32psu_1_S5_L001_R2_001_trimmed.5bp_3prime_ 100% 306KB 306.0KB/s 00:00
CTRL_16C_26psu_2_S21_L002_R1_001_trimmed.5bp_ 100% 311KB 310.6KB/s 00:00
Sealice_F1_S20_L001_R2_001_trimmed.5bp_3prime 100% 306KB 306.2KB/s 00:00
16C_32psu_4_S4_L002_R1_001_trimmed.5bp_3prime 100% 419KB 419.0KB/s 00:00
8C_32psu_4_S8_L001_R2_001_trimmed.5bp_3prime_ 100% 308KB 307.5KB/s 00:00
16C_26psu_3_S15_L001_R2_001_trimmed.5bp_3prim 100% 315KB 315.0KB/s 00:00
CTRL_8C_26psu_2_S18_L001_R2_001_trimmed.5bp_3 100% 413KB 412.8KB/s 00:00
16C_26psu_2_S14_L001_R1_001_trimmed.5bp_3prim 100% 311KB 310.6KB/s 00:00
CTRL_8C_26psu_2_S18_L002_R1_001_trimmed.5bp_3 100% 317KB 317.5KB/s 00:00
8C_26psu_2_S10_L002_R2_001_trimmed.5bp_3prime 100% 317KB 317.1KB/s 00:00
Sealice_F1_S20_L002_R2_001_trimmed.5bp_3prime 100% 425KB 425.1KB/s 00:00
8C_26psu_1_S9_L002_R2_001_trimmed.5bp_3prime_ 100% 425KB 424.9KB/s 00:00
8C_26psu_4_S12_L002_R1_001_trimmed.5bp_3prime 100% 424KB 423.6KB/s 00:00
16C_32psu_2_S2_L001_R1_001_trimmed.5bp_3prime 100% 416KB 415.8KB/s 00:00
8C_32psu_4_S8_L001_R2_001_trimmed.5bp_3prime_ 100% 420KB 419.7KB/s 00:00
16C_26psu_1_S13_L002_R1_001_trimmed.5bp_3prim 100% 425KB 425.2KB/s 00:00
CTRL_8C_26psu_2_S18_L002_R1_001_trimmed.5bp_3 100% 428KB 427.9KB/s 00:00
16C_32psu_3_S3_L001_R1_001_trimmed.5bp_3prime 100% 416KB 416.1KB/s 00:00
Sealice_F2_S22_L001_R2_001_trimmed.5bp_3prime 100% 422KB 421.9KB/s 00:00
Sealice_F1_S20_L001_R1_001_trimmed.5bp_3prime 100% 299KB 299.0KB/s 00:00
CTRL_16C_26psu_2_S21_L002_R2_001_trimmed.5bp_ 100% 413KB 413.3KB/s 00:00
8C_26psu_1_S9_L002_R2_001_trimmed.5bp_3prime_ 100% 314KB 314.2KB/s 00:00
16C_26psu_2_S14_L002_R1_001_trimmed.5bp_3prim 100% 424KB 424.4KB/s 00:01
8C_32psu_2_S6_L001_R1_001_trimmed.5bp_3prime_ 100% 308KB 307.6KB/s 00:00
8C_32psu_2_S6_L001_R1_001_trimmed.5bp_3prime_ 100% 417KB 417.1KB/s 00:00
16C_26psu_2_S14_L001_R2_001_trimmed.5bp_3prim 100% 305KB 305.2KB/s 00:00
8C_32psu_2_S6_L001_R2_001_trimmed.5bp_3prime_ 100% 304KB 303.8KB/s 00:00
16C_26psu_2_S14_L002_R1_001_trimmed.5bp_3prim 100% 311KB 310.8KB/s 00:00
8C_32psu_4_S8_L001_R1_001_trimmed.5bp_3prime_ 100% 306KB 306.3KB/s 00:00
8C_26psu_1_S9_L001_R2_001_trimmed.5bp_3prime_ 100% 424KB 424.5KB/s 00:00
CTRL_16C_26psu_1_S19_L002_R2_001_trimmed.5bp_ 100% 314KB 314.2KB/s 00:00
16C_32psu_3_S3_L002_R1_001_trimmed.5bp_3prime 100% 306KB 305.9KB/s 00:00
8C_26psu_2_S10_L002_R1_001_trimmed.5bp_3prime 100% 309KB 309.0KB/s 00:00
Sealice_F2_S22_L001_R1_001_trimmed.5bp_3prime 100% 417KB 417.2KB/s 00:00
8C_26psu_4_S12_L002_R2_001_trimmed.5bp_3prime 100% 422KB 421.9KB/s 00:00
16C_32psu_4_S4_L002_R2_001_trimmed.5bp_3prime 100% 322KB 322.4KB/s 00:00
CTRL_16C_26psu_2_S21_L001_R2_001_trimmed.5bp_ 100% 306KB 305.8KB/s 00:00
CTRL_8C_26psu_2_S18_L002_R2_001_trimmed.5bp_3 100% 307KB 307.5KB/s 00:00
8C_32psu_3_S7_L002_R1_001_trimmed.5bp_3prime_ 100% 422KB 422.0KB/s 00:00
16C_26psu_1_S13_L002_R2_001_trimmed.5bp_3prim 100% 424KB 423.9KB/s 00:00
8C_26psu_4_S12_L001_R2_001_trimmed.5bp_3prime 100% 417KB 417.1KB/s 00:00
8C_32psu_3_S7_L001_R2_001_trimmed.5bp_3prime_ 100% 314KB 314.1KB/s 00:00
16C_26psu_4_S16_L001_R1_001_trimmed.5bp_3prim 100% 419KB 418.7KB/s 00:00
16C_32psu_3_S3_L002_R1_001_trimmed.5bp_3prime 100% 418KB 418.4KB/s 00:00
Sealice_F1_S20_L002_R1_001_trimmed.5bp_3prime 100% 299KB 298.8KB/s 00:00
16C_32psu_3_S3_L001_R2_001_trimmed.5bp_3prime 100% 422KB 421.6KB/s 00:00
CTRL_8C_26psu_1_S17_L002_R1_001_trimmed.5bp_3 100% 304KB 304.0KB/s 00:00
CTRL_8C_26psu_1_S17_L001_R2_001_trimmed.5bp_3 100% 426KB 425.6KB/s 00:00
16C_32psu_2_S2_L002_R2_001_trimmed.5bp_3prime 100% 317KB 317.3KB/s 00:00
8C_26psu_3_S11_L002_R2_001_trimmed.5bp_3prime 100% 316KB 315.6KB/s 00:00
16C_32psu_2_S2_L001_R1_001_trimmed.5bp_3prime 100% 303KB 302.8KB/s 00:00
8C_32psu_2_S6_L002_R1_001_trimmed.5bp_3prime_ 100% 308KB 307.7KB/s 00:00
16C_32psu_3_S3_L001_R1_001_trimmed.5bp_3prime 100% 305KB 305.1KB/s 00:01
16C_26psu_3_S15_L002_R2_001_trimmed.5bp_3prim 100% 323KB 323.4KB/s 00:00
CTRL_16C_26psu_1_S19_L001_R1_001_trimmed.5bp_ 100% 419KB 419.5KB/s 00:00
CTRL_16C_26psu_1_S19_L001_R2_001_trimmed.5bp_ 100% 306KB 306.0KB/s 00:00
16C_26psu_4_S16_L002_R2_001_trimmed.5bp_3prim 100% 424KB 423.9KB/s 00:00
8C_32psu_3_S7_L001_R1_001_trimmed.5bp_3prime_ 100% 417KB 416.9KB/s 00:00
16C_26psu_1_S13_L001_R2_001_trimmed.5bp_3prim 100% 315KB 314.8KB/s 00:00
CTRL_8C_26psu_2_S18_L001_R2_001_trimmed.5bp_3 100% 309KB 309.0KB/s 00:00
16C_32psu_4_S4_L002_R1_001_trimmed.5bp_3prime 100% 305KB 305.0KB/s 00:00
8C_32psu_4_S8_L002_R1_001_trimmed.5bp_3prime_ 100% 308KB 307.9KB/s 00:00
8C_26psu_1_S9_L002_R1_001_trimmed.5bp_3prime_ 100% 311KB 310.7KB/s 00:00
16C_32psu_1_S1_L002_R1_001_trimmed.5bp_3prime 100% 433KB 432.6KB/s 00:00
CTRL_16C_26psu_2_S21_L002_R1_001_trimmed.5bp_ 100% 421KB 420.7KB/s 00:00
16C_26psu_3_S15_L002_R1_001_trimmed.5bp_3prim 100% 318KB 317.5KB/s 00:00
8C_26psu_4_S12_L001_R2_001_trimmed.5bp_3prime 100% 303KB 303.1KB/s 00:00
Sealice_F2_S22_L002_R1_001_trimmed.5bp_3prime 100% 306KB 306.3KB/s 00:00
8C_32psu_1_S5_L001_R1_001_trimmed.5bp_3prime_ 100% 416KB 416.5KB/s 00:00
16C_26psu_4_S16_L002_R2_001_trimmed.5bp_3prim 100% 314KB 313.5KB/s 00:00
CTRL_8C_26psu_2_S18_L001_R1_001_trimmed.5bp_3 100% 310KB 309.9KB/s 00:00
Sealice_F2_S22_L002_R2_001_trimmed.5bp_3prime 100% 310KB 309.7KB/s 00:00
CTRL_16C_26psu_1_S19_L002_R1_001_trimmed.5bp_ 100% 426KB 425.8KB/s 00:00
8C_26psu_1_S9_L002_R1_001_trimmed.5bp_3prime_ 100% 424KB 423.6KB/s 00:00
Sealice_F2_S22_L002_R2_001_trimmed.5bp_3prime 100% 423KB 423.3KB/s 00:00
16C_32psu_4_S4_L001_R1_001_trimmed.5bp_3prime 100% 419KB 418.8KB/s 00:00
CTRL_8C_26psu_1_S17_L002_R2_001_trimmed.5bp_3 100% 424KB 424.3KB/s 00:00
CTRL_16C_26psu_1_S19_L002_R2_001_trimmed.5bp_ 100% 424KB 424.3KB/s 00:00
CTRL_16C_26psu_2_S21_L002_R2_001_trimmed.5bp_ 100% 311KB 310.7KB/s 00:00
16C_26psu_2_S14_L002_R2_001_trimmed.5bp_3prim 100% 425KB 425.1KB/s 00:00
8C_32psu_1_S5_L002_R1_001_trimmed.5bp_3prime_ 100% 310KB 309.8KB/s 00:00
8C_26psu_1_S9_L001_R1_001_trimmed.5bp_3prime_ 100% 419KB 419.2KB/s 00:01
8C_26psu_3_S11_L002_R2_001_trimmed.5bp_3prime 100% 426KB 425.9KB/s 00:00
8C_32psu_4_S8_L002_R2_001_trimmed.5bp_3prime_ 100% 423KB 423.5KB/s 00:00
8C_32psu_4_S8_L001_R1_001_trimmed.5bp_3prime_ 100% 415KB 414.9KB/s 00:00
8C_32psu_2_S6_L002_R2_001_trimmed.5bp_3prime_ 100% 420KB 420.3KB/s 00:00
Sealice_F2_S22_L001_R1_001_trimmed.5bp_3prime 100% 303KB 303.1KB/s 00:00
8C_26psu_4_S12_L002_R1_001_trimmed.5bp_3prime 100% 311KB 310.7KB/s 00:00
CTRL_8C_26psu_1_S17_L001_R1_001_trimmed.5bp_3 100% 420KB 419.6KB/s 00:00
8C_32psu_1_S5_L001_R1_001_trimmed.5bp_3prime_ 100% 307KB 307.1KB/s 00:00
8C_32psu_1_S5_L002_R2_001_trimmed.5bp_3prime_ 100% 308KB 308.0KB/s 00:00
16C_26psu_1_S13_L001_R1_001_trimmed.5bp_3prim 100% 421KB 420.9KB/s 00:00
CTRL_16C_26psu_1_S19_L001_R2_001_trimmed.5bp_ 100% 418KB 418.3KB/s 00:00
8C_32psu_3_S7_L002_R1_001_trimmed.5bp_3prime_ 100% 310KB 310.3KB/s 00:00
8C_26psu_2_S10_L001_R2_001_trimmed.5bp_3prime 100% 307KB 306.6KB/s 00:00
16C_26psu_3_S15_L002_R2_001_trimmed.5bp_3prim 100% 427KB 426.8KB/s 00:00
16C_26psu_4_S16_L001_R1_001_trimmed.5bp_3prim 100% 309KB 308.5KB/s 00:00
16C_26psu_1_S13_L001_R1_001_trimmed.5bp_3prim 100% 312KB 312.0KB/s 00:00
CTRL_8C_26psu_2_S18_L002_R2_001_trimmed.5bp_3 100% 418KB 418.1KB/s 00:00
8C_26psu_3_S11_L001_R2_001_trimmed.5bp_3prime 100% 420KB 420.5KB/s 00:00
8C_26psu_3_S11_L002_R1_001_trimmed.5bp_3prime 100% 420KB 420.5KB/s 00:00
8C_26psu_4_S12_L001_R1_001_trimmed.5bp_3prime 100% 308KB 308.4KB/s 00:00
16C_26psu_1_S13_L002_R1_001_trimmed.5bp_3prim 100% 314KB 313.7KB/s 00:00
16C_32psu_1_S1_L001_R2_001_trimmed.5bp_3prime 100% 423KB 423.3KB/s 00:00
16C_26psu_3_S15_L001_R1_001_trimmed.5bp_3prim 100% 318KB 318.0KB/s 00:00
8C_32psu_1_S5_L001_R2_001_trimmed.5bp_3prime_ 100% 419KB 418.6KB/s 00:00
8C_32psu_4_S8_L002_R2_001_trimmed.5bp_3prime_ 100% 319KB 318.9KB/s 00:00
CTRL_16C_26psu_2_S21_L001_R1_001_trimmed.5bp_ 100% 315KB 315.2KB/s 00:00
8C_26psu_3_S11_L001_R2_001_trimmed.5bp_3prime 100% 310KB 310.0KB/s 00:01
8C_32psu_2_S6_L002_R1_001_trimmed.5bp_3prime_ 100% 421KB 420.8KB/s 00:00
16C_26psu_1_S13_L001_R2_001_trimmed.5bp_3prim 100% 425KB 425.5KB/s 00:00
8C_32psu_1_S5_L002_R1_001_trimmed.5bp_3prime_ 100% 422KB 421.7KB/s 00:00
16C_32psu_3_S3_L001_R2_001_trimmed.5bp_3prime 100% 316KB 316.4KB/s 00:00
8C_26psu_1_S9_L001_R2_001_trimmed.5bp_3prime_ 100% 314KB 313.7KB/s 00:00
16C_26psu_3_S15_L002_R1_001_trimmed.5bp_3prim 100% 428KB 428.2KB/s 00:00
8C_26psu_2_S10_L001_R1_001_trimmed.5bp_3prime 100% 313KB 312.6KB/s 00:00
CTRL_16C_26psu_2_S21_L001_R1_001_trimmed.5bp_ 100% 420KB 420.3KB/s 00:00
CTRL_16C_26psu_1_S19_L002_R1_001_trimmed.5bp_ 100% 316KB 316.0KB/s 00:00
Sealice_F1_S20_L001_R2_001_trimmed.5bp_3prime 100% 422KB 421.7KB/s 00:00
16C_32psu_1_S1_L001_R1_001_trimmed.5bp_3prime 100% 424KB 424.4KB/s 00:00
16C_26psu_4_S16_L001_R2_001_trimmed.5bp_3prim 100% 421KB 421.2KB/s 00:00
CTRL_16C_26psu_2_S21_L001_R2_001_trimmed.5bp_ 100% 415KB 415.2KB/s 00:00
16C_32psu_1_S1_L001_R2_001_trimmed.5bp_3prime 100% 312KB 312.1KB/s 00:00
8C_26psu_2_S10_L002_R2_001_trimmed.5bp_3prime 100% 425KB 424.6KB/s 00:00
Sealice_F2_S22_L001_R2_001_trimmed.5bp_3prime 100% 307KB 307.3KB/s 00:00
8C_32psu_3_S7_L001_R2_001_trimmed.5bp_3prime_ 100% 424KB 424.4KB/s 00:00
STEP 6. run multiqc
srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ multiqc .
[INFO ] multiqc : This is MultiQC v0.9
[INFO ] multiqc : Template : default
[INFO ] multiqc : Searching '.'
[INFO ] fastqc : Found 88 reports
[INFO ] multiqc : Report : multiqc_report.html
[INFO ] multiqc : Data : multiqc_data
[INFO ] multiqc : MultiQC complete
STEP 7. copy back to Gannet via ostrich
srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ ls
FASTQC multiqc_data multiqc_report.html
srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ mv multiqc_report.html multiqc_data/
srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ ls
FASTQC multiqc_data
srlab@emu:~/GitHub/Shelly_Pgenerosa/multiqc$ scp -r multiqc_data/ strigg@ostrich.fish.washington.edu:/Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_1st5bp/FASTQC
Password:
multiqc_report.html 100% 1842KB 1.8MB/s 00:00
.multiqc.log 100% 7012 6.9KB/s 00:00
multiqc_sources.txt 100% 15KB 15.2KB/s 00:00
multiqc_general_stats.txt 100% 8352 8.2KB/s 00:00
multiqc_fastqc.txt 100% 22KB 22.0KB/s 00:00
STEP 8. check multiqc report - multiqc report here: https://gannet.fish.washington.edu/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_1st5bp/FASTQC/multiqc_data/multiqc_report.html
CONCLUSIONS:
- blunt trimming seemed to work and removes the 5bp in the 5’ of both reads that seem to be random primer
- MultiQC analyses compared:
- doesn’t seem to be any obvious difference between L001 and L002 so should be OK to combine them.
Next steps:
- start mox job for concatenating L001 and L002 files
- script here: https://gannet.fish.washington.edu/metacarcinus/mox_jobs/20190805_Concat_L1_L2_SalmoCalig.sh
- this got delayed because of node maintenance
- start mox job for testing alignment parameters