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advice on some features #24
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Hi @dcruz5h Thanks for your interest in our tool!
Currently, we only support Truseq adapters. I can add a new parameter to support trimming with the Nextera adaptors later. |
Thank you for the answer. It will be great if you can add an option for Nextera adaptors as bulk CUT$Tag works with these adaptors and not Truseq. |
Hi, we have already supported the Nextera adaptors processing with the bulk data, please update the software to the least. Please let me know if you encounter any trouble with this. Usage: |
Thank you !! I just finish running it and it now trims neuter adaptors. It is able to generate bam files as well as bed files. |
Awesome! I will close this thread, please feel free to open new issues if you run into any issues. |
Thank you for all the work you put on this pipeline.
I hope you can help me define some parameters. I am running the pipeline for bulk Cut and Tag samples that were sequenced pairs end with 150Cycle kit.
What would the fastq_sequence_length be?
What does frag_120 do ? if you do FALSE what happens to the bam file ? and if you do TRUE what happens ?
The initial step of adaptor trimming, trimomatic assumed my fastq files had Truseq adapters even after I specify CUT&Tag as the experiment_type. How can I change trimomatic to remove Nextera adaptors instead ?
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