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Dear all,
I received my HiSeq Illumina RNAseq data and want to run trimmomatic to remove bad quality reads and trim adapters. I have used trimmomatic before but I am currently in doubt if I create the adapter file in a correct way, can someone please correct me if I'm wrong?
Sequencing happened on Illumina HiSeq4000 using NEBnext kit for the library construction.
From the sequencing facility I have received the adapter and index sequences (e.g for my first sample):
Adapter:
5' Adapter: 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'
3' Adapter(lowercase 6bp bases is Index) 5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCACatcacgATCTCGTATGCCGTCTTCTGCTTG-3
index:
CTGGCATA;CGGCTATG
- I do not understand why I receive two indexes for a single sample? A single sample, needs only one adapter with one specific index? Correct?
- Trimmomatic needs an adapter file and I will create as follows (with all adapters and indeces in a single file):
>Prefix_AdapterPE1/1
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Prefix_AdapterPE1/2
GATCGGAAGAGCACACGTCTGAACTCCAGTCACctggcataATCTCGTATGCCGTCTTCTGCTTG
With the index in capitals also, but just to show that I will manually add the index sequence. I will do this for all received index sequences, added to a single adapter file and will finally run Trimmomatic.
Any comments are welcome!
I received my HiSeq Illumina RNAseq data and want to run trimmomatic to remove bad quality reads and trim adapters. I have used trimmomatic before but I am currently in doubt if I create the adapter file in a correct way, can someone please correct me if I'm wrong?
Sequencing happened on Illumina HiSeq4000 using NEBnext kit for the library construction.
From the sequencing facility I have received the adapter and index sequences (e.g for my first sample):
Adapter:
5' Adapter: 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'
3' Adapter(lowercase 6bp bases is Index) 5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCACatcacgATCTCGTATGCCGTCTTCTGCTTG-3
index:
CTGGCATA;CGGCTATG
- I do not understand why I receive two indexes for a single sample? A single sample, needs only one adapter with one specific index? Correct?
- Trimmomatic needs an adapter file and I will create as follows (with all adapters and indeces in a single file):
>Prefix_AdapterPE1/1
AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
>Prefix_AdapterPE1/2
GATCGGAAGAGCACACGTCTGAACTCCAGTCACctggcataATCTCGTATGCCGTCTTCTGCTTG
With the index in capitals also, but just to show that I will manually add the index sequence. I will do this for all received index sequences, added to a single adapter file and will finally run Trimmomatic.
Any comments are welcome!