I am doing sequence alignment for Matt (Su'ad and Josh's) transcriptomic/RNA seq data. I have downloaded the first part of the data and this is saved in: /uufs/chpc.utah.edu/common/home/gompert-group1/data/lycaeides/matt_transcriptome/MelissaRNA_diet
I have now downloaded the second part of the data and this is also saved in the folder on the cluster.
Total 24 fastq files.
-f ../../fast_genome/re_mod_map_timema_06Jun2016_RvNkF702.fasta
TruSeq Adapter, Index 10 -> I got this from the illumina website. I first looked at this in the fastQC and got the TruSeq Adapter Index 10 info from there.
5’ GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG
**Note you have to give the -Q33 flag for illumina reads, otherwise fastx does not work.
Options used for adapter trimming: cat $i | ../../fastX/bin/fastq_to_fasta -Q33 -n | ../../fastX/bin/fastx_clipper -Q33 -l 15 -a GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTTATCTCGTATGCCGTCTTCTGCTTG | ../../fastX/bin/fastx_trimmer -Q33 -f 1 -l 27 | ../../fastX/bin/fastx_collapser > ${i}.final.fa
Reads before adapter trimming:
162618100 KS001_S71_L008_R1_001.fastq
162618100 KS001_S71_L008_R2_001.fastq
153812656 KS002_S72_L008_R1_001.fastq
153812656 KS002_S72_L008_R2_001.fastq
156068828 KS003_S73_L008_R1_001.fastq
156068828 KS003_S73_L008_R2_001.fastq
128006008 KS004_S74_L008_R1_001.fastq
4350249 KS004_S74_L008_R2_001.fastq
200995944 PMKS001_S109_L007_R1_001.fastq
200995944 PMKS001_S109_L007_R2_001.fastq
169247068 PMKS002_S110_L007_R1_001.fastq
169247068 PMKS002_S110_L007_R2_001.fastq
172033908 PMKS003_S111_L007_R1_001.fastq
172033908 PMKS003_S111_L007_R2_001.fastq
217293664 PMKS004_S112_L007_R1_001.fastq
217293664 PMKS004_S112_L007_R2_001.fastq
215729044 PMKS005_S113_L007_R1_001.fastq
215729044 PMKS005_S113_L007_R2_001.fastq
168477920 PMKS006_S114_L007_R1_001.fastq
168477920 PMKS006_S114_L007_R2_001.fastq
258095776 PMKS007_S115_L007_R1_001.fastq
258095776 PMKS007_S115_L007_R2_001.fastq
190216896 PMKS008_S116_L007_R1_001.fastq
190216896 PMKS008_S116_L007_R2_001.fastq
4261535865 total
Reads after adapter trimming:
7154400 KS001_S71_L008_R1_001.fastq.final.fa
14318514 KS001_S71_L008_R2_001.fastq.final.fa
5548254 KS002_S72_L008_R1_001.fastq.final.fa
11711874 KS002_S72_L008_R2_001.fastq.final.fa
5247366 KS003_S73_L008_R1_001.fastq.final.fa
11589924 KS003_S73_L008_R2_001.fastq.final.fa
6355348 KS004_S74_L008_R1_001.fastq.final.fa
1052106 KS004_S74_L008_R2_001.fastq.final.fa
13597390 PMKS001_S109_L007_R1_001.fastq.final.fa
17056392 PMKS001_S109_L007_R2_001.fastq.final.fa
12680260 PMKS002_S110_L007_R1_001.fastq.final.fa
15968068 PMKS002_S110_L007_R2_001.fastq.final.fa
10327208 PMKS003_S111_L007_R1_001.fastq.final.fa
12915420 PMKS003_S111_L007_R2_001.fastq.final.fa
13743426 PMKS004_S112_L007_R1_001.fastq.final.fa
16825006 PMKS004_S112_L007_R2_001.fastq.final.fa
14649986 PMKS005_S113_L007_R1_001.fastq.final.fa
18772886 PMKS005_S113_L007_R2_001.fastq.final.fa
11967728 PMKS006_S114_L007_R1_001.fastq.final.fa
14867654 PMKS006_S114_L007_R2_001.fastq.final.fa
17606924 PMKS007_S115_L007_R1_001.fastq.final.fa
22427804 PMKS007_S115_L007_R2_001.fastq.final.fa
14138122 PMKS008_S116_L007_R1_001.fastq.final.fa
17684458 PMKS008_S116_L007_R2_001.fastq.final.fa
308206518 total