Does sim3C accept self-prepared community abundance profile in Hi-C mode?

[zengxiaofei]

Hi Matthew,

I gave sim3C a self-prepared community abundance profile in Hi-C mode like this:

$ sim3C rice_genome_chr0102.fa sim.fastq --profile mycom.txt --dist uniform -n 25000000 -l 150 -e MboI -m hic --seed 12345

mycom.txt:

#chrom  cell    abundance   copy_number
9311_Chr01  cell1   0.25    1
9311_Chr02  cell1   0.25    1
Nipponbare_Chr01    cell1   0.25    1
Nipponbare_Chr02    cell1   0.25    1

But sim3C generated a new profile.tsv in which cell & abundance are different from mycom.txt:

#chrom  cell    abundance   copy_number
9311_Chr01  9311_Chr01  0.568757    1
9311_Chr02  9311_Chr02  0.193565    1
Nipponbare_Chr01    Nipponbare_Chr01    0.112525    1
Nipponbare_Chr02    Nipponbare_Chr02    0.125154    1

So I have no idea whether my profile has been adopted.

Another question is will sim3C simulate inter-chromosome contacts in Hi-C mode?

Thanks! :smile: Xiaofei

[cerebis]

Sorry Xiaofei, you've found a bit of a usability bug.

If you provide a user-based profile, don't use the --dist uniform option. In doing so, you're asking sim3C to create a profile and use the file-name you provided.

So, for your case, just provide the profile file-name.

Regards, Matt DeMaere

On Fri, 25 Mar 2022 at 14:42, Xiaofei Zeng @.***> wrote:

Hi Matthew,

I gave sim3C a self-prepared community abundance profile in Hi-C mode like this:

$ sim3C rice_genome_chr0102.fa sim.fastq --profile mycom.txt --dist uniform -n 25000000 -l 150 -e MboI -m hic --seed 12345

mycom.txt:

chrom cell abundance copy_number

9311_Chr01 cell1 0.25 1

9311_Chr02 cell1 0.25 1

Nipponbare_Chr01 cell1 0.25 1

Nipponbare_Chr02 cell1 0.25 1

But sim3C generated a new profile.tsv in which cell & abundance are different from mycom.txt:

chrom cell abundance copy_number

9311_Chr01 9311_Chr01 0.568757 1

9311_Chr02 9311_Chr02 0.193565 1

Nipponbare_Chr01 Nipponbare_Chr01 0.112525 1

Nipponbare_Chr02 Nipponbare_Chr02 0.125154 1

So I have no idea whether my profile has been adopted.

Another question is will sim3C simulate inter-chromosome contacts in Hi-C mode?

Thanks! 😄 Xiaofei

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[zengxiaofei]

I got it! Thank you!