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Old 05-16-2020, 12:50 PM   #1
iramai
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Location: Eibar

Join Date: Mar 2018
Posts: 6
Default How to trim dual index adapters with Trim Galore!

Hi everybody,
I am trying to trim some adapters with Trim Galore from my bisulfite sequencing data, but I don't know what command to use.
It has been really difficult to take the information of library construction and I only know that it has been done using IDT unique dual indexing adapters in paired end data, detailed as follows:

1 - P5 ATATGCGC, P7 CTGATCGT
30 - P5 AACGTCTG, P7 GCGTCATT
31 - P5 TATCGGTC, P7 ATCCGGTA
32 - P5 CGCTCTAT, P7 CGTTGCAA

When doing the FASTQC analysis I have found some overrepresented sequences such as:
- In one of the sequence of the pair
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
- In the other sequence of the pair
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT

An also in the adapter content section the Illumina Universal adapters are identified

Does all this make sense?
So I need to add something more to those P5 and P7 adapter sequences when running Trim Galore?

Will this command be correct for the first example of unique dual index adapters?

> trim_galore --paired -a ATATGCGC -a2 CTGATCGT -q 15 --stringency 5 -e 0.05 --length 50 --fastqc --gzip file_1.fastq.gz file_2.fastq.gz

Thanks in advance!
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