Which bam generated from `HiC-Pro` should be fed to `yahs`

[leon945945]

Hi, accroding to your tutorial, I generated bam files by HiC-Pro:

GB_HiC_1_GBhap1-bowtie2.bwt2merged.bam
GB_HiC_2_GBhap1-bowtie2.bwt2merged.bam
GB_HiC_GBhap1-bowtie2.bwt2pairs.bam

three bams were produced in bwt2 directory, but I don't know which one should be fed to yahs
Could you please give me some advances.

[WWz33]

same issue

[c-zhou]

Hi @WWz33,

I am not familiar with the HiC-Pro pipeline. Based on the file names, it looks like GB_HiC_[12]_GBhap1-bowtie2.bwt2merged.bam are for Hi-C read 1 and read 2 respectively, while GB_HiC_GBhap1-bowtie2.bwt2pairs.bam contains both reads after merging the two files. If that is the case, the latter should be used as the input for YaHS.

You will want to double-check this, or you can post a few lines from each of these files here, and I can take a look.

Best,
Chenxi

[WWz33]

Hi chen
HiC-Pro_result.md.
Thank you for your reply, here is the explanation of the HIC-pro results. I noticed that many pipelines use .bwt2pairs.bam, but this is only the result of merging dual alignments, not the filtered result of HIC-pro. As mentioned in the md above, .allValidPairs is the filtered result.
I used
awk '{print $1"\t"$2"\t"$3"\t"$5"\t"$6}' hic_results/data/sample/sample.allValidPairs > hic.pa5
yahs nuclear.fa hic.pa5,
which ran good.
However, I'm not sure if this is correct. If you need it, I would be happy to transfer my result files to you.
https://github.com/nservant/HiC-Pro/blob/57a0bf2cb1d7ebeb44b4f11e78058b504260c5c9/scripts/mapped_2hic_fragments.py#L408

-rw-r--r-- 1 sri2025201067 hejianbo_sri    0 Jun 30 16:28 A01_nuclear.bwt2pairs.SinglePairs ##
-rw-r--r-- 1 sri2025201067 hejianbo_sri    0 Jun 30 16:28 A01_nuclear.bwt2pairs.FiltPairs
-rw-r--r-- 1 sri2025201067 hejianbo_sri 755M Jun 30 17:25 A01_nuclear.bwt2pairs.DEPairs ## Dangling End
-rw-r--r-- 1 sri2025201067 hejianbo_sri 201M Jun 30 17:25 A01_nuclear.bwt2pairs.REPairs ##  Religation
-rw-r--r-- 1 sri2025201067 hejianbo_sri 328M Jun 30 17:25 A01_nuclear.bwt2pairs.SCPairs ## Self Circle
-rw-r--r-- 1 sri2025201067 hejianbo_sri 4.5M Jun 30 17:25 A01_nuclear.bwt2pairs.DumpPairs ## Dumped
-rw-r--r-- 1 sri2025201067 hejianbo_sri  329 Jun 30 17:25 A01_nuclear.bwt2pairs.RSstat 
-rw-r--r-- 1 sri2025201067 hejianbo_sri  20G Jun 30 17:28 A01_nuclear.bwt2pairs.validPairs
-rw-r--r-- 1 sri2025201067 hejianbo_sri  20G Jun 30 17:30 sample.allValidPairs

(base) sri2025201067@sri-test-01:~/vs_genome/gx_8/raw_data/hic/nuclear_hicpro/hicpro_output/hic_results/data/sample$ cat  A01_nuclear.bwt2pairs.RSstat 
## Hi-C processing
Valid_interaction_pairs	165526636
Valid_interaction_pairs_FF	41356000
Valid_interaction_pairs_RR	41337200
Valid_interaction_pairs_RF	41184957
Valid_interaction_pairs_FR	41648479
Dangling_end_pairs	6237374
Religation_pairs	1649322
Self_Cycle_pairs	2702718
Single-end_pairs	0
Filtered_pairs	0
Dumped_pairs	36059

(base) sri2025201067@sri-test-01:~/vs_genome/gx_8/raw_data/hic/nuclear_hicpro/hicpro_output/hic_results/data/sample$ head sample.allValidPairs 
E250188287L1C010R03004305735/2	ptg000001l	13248	+	ptg000001l	572249	-	294	HIC_ptg000001l_1	HIC_ptg000001l_1383	42	38	
E250188287L1C016R02304415633/1	ptg000001l	13253	+	ptg000014l	9927	+	362	HIC_ptg000001l_1	HIC_ptg000014l_11	35	39	
E250188521L1C011R03802289810/1	ptg000001l	13253	+	ptg000028l	16858813	-	391	HIC_ptg000001l_1	HIC_ptg000028l_41117	35	39	
E250188287L1C023R03603495749/1	ptg000001l	13255	+	ptg000001l	8065561	+	321	HIC_ptg000001l_1	HIC_ptg000001l_19383	35	42	
E250188287L1C025R02603389806/1	ptg000001l	13255	+	ptg000017l	8956447	+	254	HIC_ptg000001l_1	HIC_ptg000017l_20982	35	42	
E250188287L1C021R01001172660/2	ptg000001l	13257	+	ptg000011l	12309417	+	277	HIC_ptg000001l_1	HIC_ptg000011l_30626	37	42	
E250188287L1C038R01304720294/2	ptg000001l	13257	+	ptg000013l	34008310	+	329	HIC_ptg000001l_1	HIC_ptg000013l_87164	36	42	
E250188287L1C018R00304949799/2	ptg000001l	13259	+	ptg000001l	1725186	-	430	HIC_ptg000001l_1	HIC_ptg000001l_4116	37	42	
E250188287L1C026R01501719390/1	ptg000001l	13260	+	ptg000025l	8802109	+	195	HIC_ptg000001l_1	HIC_ptg000025l_21979	35	42	
E250188287L1C024R00603921428/2	ptg000001l	13261	+	ptg000031l	21888889	-	310	HIC_ptg000001l_1	HIC_ptg000031l_55115	35	42	

Best!

[c-zhou]

Thanks for the explanation @WWz33. You are absolutely right. The sample.allValidPairs - with your conversion to pa5 - is the correct one to use.

Chenxi

[WWz33]

Hi,Chenxi!
Thank you very much, your reply has been extremely helpful in my learning process!
Best~