phred score per base sequence quality

Question

[yueli7]

Hello,

I have RNA sequencing data. After running FastQc, it comes out bad result.

Do I need to fix it?

Thanks in advance for any great help!

Best,

Yue

Answer 1

[hafiz.talhamalik]

only the quality of 1st base is bad. rest is fine. you can simply trim that.. and I think only one base not gonna cause many problems..!!

[yueli7]

Hello hafiz.talhamalik,

Thank you so much for your help!

li@li-HP-P:~/Trimmomatic-0.39$ java -jar trimmomatic-0.39.jar PE P01_1.txt.gz P01_2.txt.gz P01_1_paired.fastq.gz P01_1_unpaired.fastq.gz P01_2_paired.fastq.gz P01_2_unpaired.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:18 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
TrimmomaticPE: Started with arguments:
P01_1.txt.gz P01_2.txt.gz P01_1_paired.fastq.gz P01_1_unpaired.fastq.gz P01_2_paired.fastq.gz P01_2_unpaired.fastq.gz ILLUMINACLIP:NexteraPE-PE.fa:2:30:10 LEADING:18 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Using PrefixPair: 'AGATGTGTATAAGAGACAG' and 'AGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTCCGAGCCCACGAGAC'
Using Long Clipping Sequence: 'CTGTCTCTTATACACATCTGACGCTGCCGACGA'
ILLUMINACLIP: Using 1 prefix pairs, 4 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences
Quality encoding detected as phred33
Input Read Pairs: 85895601 Both Surviving: 61758053 (71.90%) Forward Only Surviving: 23407882 (27.25%)         Reverse Only Surviving: 283767 (0.33%) Dropped: 445899 (0.52%)
TrimmomaticPE: Completed successfully