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advice on some features #24

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dcruz5h opened this issue Aug 16, 2021 · 5 comments
Closed

advice on some features #24

dcruz5h opened this issue Aug 16, 2021 · 5 comments

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@dcruz5h
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dcruz5h commented Aug 16, 2021

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 ?

@fl-yu
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fl-yu commented Aug 19, 2021

Hi @dcruz5h Thanks for your interest in our tool!
I do not know what the sequence length will be for 150Cycle kit. But I think it is ok if the read length is longer than 25bp as our two-step trimming will eventually trim all the reads to 25bp and we showed that this trimming strategy is able to improve reads alignment.
If you specify frag_120 as TRUE, the bam file will be filtered with the fragments longer than 120, we recommend it when you do a typical TF experiment.

[frag_120]: Whether filter the bam files based on the criteria of fragment size 120
			options: TRUE (default) or FALSE 

Currently, we only support Truseq adapters. I can add a new parameter to support trimming with the Nextera adaptors later.

@dcruz5h
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dcruz5h commented Aug 19, 2021

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.

@fl-yu
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fl-yu commented Sep 2, 2021

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:
In the new configuration file, you could value adaptor_type as Truseq or Nextera to specify your adaptor type.
"adaptor_type":"Truseq" or
"adaptor_type":"Nextera"

@dcruz5h
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dcruz5h commented Sep 3, 2021

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.
Cheers

@fl-yu
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fl-yu commented Sep 3, 2021

Awesome! I will close this thread, please feel free to open new issues if you run into any issues.

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