Differences

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--- cleaning_of_illumina_paired_end_reads [2020/12/15 06:07] – 24.138.72.240
+++ cleaning_of_illumina_paired_end_reads [2021/12/16 15:07] (current) – 170.10.250.122
@@ Line 45: / Line 45: @@
 # trimmomatic version is 0.39 (latest release)
 source activate trimmomatic
-trimmomatic PE -threads 20 -phred33 -trimlog $basename\.log $R1 $R2 $basename\.1.PT.fq $basename\.1unPT.fq \ $basename\.2.PT.fq $basename\.2.unPT.fq ILLUMINACLIP:$adap_path:2:30:10 HEADCROP:10 LEADING:10 TRAILING:10 \ SLIDINGWINDOW:40:25 MINLEN:40
+trimmomatic PE -threads 20 -phred33 -trimlog $basename\.log $R1 $R2 $basename\.1.PT.fq $basename\.1.unPT.fq $basename\.2.PT.fq $basename\.2.unPT.fq ILLUMINACLIP:$adap_path:2:30:10 HEADCROP:15 LEADING:20 TRAILING:20 SLIDINGWINDOW:40:25 MINLEN:40
+conda deactivate
 </code>
 This will perform the following:\\
-• HEADCROP: Cut the specified number (20) of bases from the start of the read.\\
+• HEADCROP: Cut the specified number (20) of bases from the start of the read. (HEADCROP:15)\\
-• LEADING: Remove bases in the start of a read if the quality is below quality 10. (LEADING:10)\\
+• LEADING: Remove bases at the start of a read if the quality is below quality 20. (LEADING:20)\\
-• TRAILING: Remove bases in the end of a read if the quality is below quality 10. (TRAILING:10)\\
+• TRAILING: Remove bases at the end of a read if the quality is below quality 20. (TRAILING:20)\\
 • SLIDINGWINDOW: Perform a sliding window trimming, cutting once the average quality within the window falls below a threshold. Scan the read with a 10-base wide sliding window, cutting when the average quality per base drops below 25 (SLIDINGWINDOW:10:25)\\
 • MINLEN: Drop the read if it is below a specified length (below 40) (MINLEN:40).\\
 • -phred33: Quality scores in Phred33 format. [https://en.wikipedia.org/wiki/FASTQ_format]\\
-• ILLUMINACLIP: Remove adapters <ILLUMINACLIP:/path/to/userdir/Adapters.fas:2:30:10> (/path/to/userdir/Adapters.fas, adapter file). \\
+• ILLUMINACLIP: Remove adapters <ILLUMINACLIP:/path/to/userdir/Adapters.fas:2:30:10> (/path/to/userdir/Adapters.fas, adapter file).\\
+  ILLUMINACLIP:<fastaWithAdaptersEtc>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold>
+  *fastaWithAdaptersEtc: specifies the path to a fasta file containing all the adapters, PCR sequences etc. The naming of the various sequences within this file determines how they are used. See below.
+  *seedMismatches: specifies the maximum mismatch count which will still allow a full match to be performed
+  *palindromeClipThreshold: specifies how accurate the match between the two 'adapter ligated' reads must be for PE palindrome read alignment.
+  *simpleClipThreshold: specifies how accurate the match between any adapter etc. sequence must be against a read.
-Parameters listed here are a little strict. You can adjust them based on your demand. To test the quality of the read, use fastqc first to get a quality control report.\\
+Parameters listed here are a little strict. You can adjust them based on your demand. To test the quality of the read, use fastqc first to get a quality control report. (More details about Trimmomatic: http://www.usadellab.org/cms/?page=trimmomatic)\\
 **3. Remove host reads: bowtie2**\\