Trimming customed adaptor sequences

timflutre / trimmomatic

Read trimming tool for Illumina NGS data.

http://www.usadellab.org/cms/index.php?page=trimmomatic

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Trimming customed adaptor sequences #17

Open Ruiqi-CUB opened 3 years ago

Ruiqi-CUB commented 3 years ago

Hello!

Is it possible to trim the customed adaptors using trimmomatic for exon capture sequencing? If so, how can I create the adaptor fasta file (sequence header etc.)?

The adapters used are below, "BCBCBCBC" stands for the barcodes.

i7: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-BCBCBCBC-ATCTCGTATGCCGTCTTCTGCTTG

i5: AATGATACGGCGACCACCGAGATCTACAC-BCBCBCBC-ACACTCTTTCCCTACACGACGCTCTTCCGATCT

Thank you in advance Best Ruiqi

taha-lang commented 3 months ago

I want to know the name of this sequence to the adapter CTGTCTCTTATACACATCT for the process of trimming, I tried by the adapter ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. But it does not work for all samples.