Differences

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--- scripts:adapter_and_quality_trimming [2025/03/10 13:37] – 37.26.174.181
+++ scripts:adapter_and_quality_trimming [2025/03/25 10:37] (current) – 37.26.174.181
@@ Line 1: / Line 1: @@
-====== How to perform quality and adapter trimming of your reads with ======
+====== How to perform quality control and adapter trimming of your reads with cutadapt and fastp ======
 ===== What to trim =====
@@ Line 169: / Line 169: @@
 This script takes the adapters, number of bases to trim, and number of threads for parallel processing as input and generates fastp reports (html, json). It operates in single-end and paired-end mode. Please note, it is important to treat your paired-end files in parallel mode, otherwise, some reads may be removed from one file, and stay in the other, which will lead to problems during alignment.
-The script will search for **Illumina Universal Adapter**. You can modify the script to select from another two available in it (just set the one you choose as the ''adapter'') or you can add yours.  It also trims polyG and polyX tails, low complexity reads.
+The script will search for **Illumina Universal Adapter**. You can modify the script to select from another two available in it (just set the one you choose as the ''adapter'') or you can add yours.  It also trims polyG and polyX tails, low complexity reads. There is also ''**-****-**detect_adapter_pe'' option, which can automatically detect adapters for paired end reads (just remove #).
 **fastp.sh**
@@ Line 252: / Line 252: @@
                       --trim_front2 "$trim_5p" --trim_tail2 "$trim_3p" \
                       --adapter_sequence "$adapter" \
+                      #--detect_adapter_pe \
                       --html "$output_dir/${filename}_fastp.html" \
                       --json "$output_dir/${filename}_fastp.json"