question about the hicstuff about instagraal HOT 4 CLOSED

Hello,
I think you are right, default alignment parameters for hicstuff are defined here: https://github.com/koszullab/hicstuff/blob/830d04fffbdb14957ba95f196d7bcdd690d84da9/hicstuff/pipeline.py#L89-L101

Generally speaking, we use local alignment because a global alignment would not allow to partially map chimeric Hi-C reads. However if you want to use different parameters, you can map the reads with whatever software / parameters you prefer and provide the output (name-sorted) BAM files to hicstuff instead of starting from fastq files.

There is a small example starting from an intermediate BAM file in the hicstuff docs: https://hicstuff.readthedocs.io/en/latest/notebooks/demo_cli.html#Starting-from-intermediate-files

I think this is what they did in the instaGRAAL paper, perhaps @baudrly or @nadegeguiglielmoni can confirm ?

Instagraal filters fragments from the Hi-C matrix with low coverage to improve results, this is the --coverage-std option. One standard dev is indeed the default value.

Hope that helps

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Hello ,
Thanks for your reply, it really helps . In other words , you just run hicstuff pipeline with the default parameters when you perform your experiment in the paper ? And not setting special parameter ? Am I right ?
Anyway , thanks for you help ,again.

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Hello,

You can indeed run the mapping step directly with hicstuff pipeline. For 150 bp reads, you should definitely use the parameter --iterative. You should also put the enzyme used for Hi-C library preparation as the parameter --enzyme. By default, the mapping tool used is bowtie2, but you can also use bwa instead if you prefer with the parameter --aligner bwa.

So if you run hicstuff on a library prepared with DpnII and using bowtie2 for mapping, the command would be:
hicstuff pipeline --enzyme DpnII --iterative --outdir hic_folder --genome assembly.fasta R1.fastq R2.fastq

You can also look at the repository with command lines used in the paper https://github.com/koszullab/ectocarpus_scripts

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Hi @nadegeguiglielmoni ,
Thanks for you links, I viewed the scripts and got to know the next step .
Have a nice day and I will close the issue.

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