Differences

This shows you the differences between two versions of the page.

--- cleaning_of_illumina_paired_end_reads [2021/12/16 15:04] – 170.10.250.122
+++ cleaning_of_illumina_paired_end_reads [2021/12/16 15:07] (current) – 170.10.250.122
@@ Line 57: / Line 57: @@
 • 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).\\
-  __Format__: ILLUMINACLIP:<fastaWithAdaptersEtc>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold>
+  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. \\
+  *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**\\