Hello, thanks for sharing thes great resource in microglia. I followed the author's pipeline to analyze microglial Hi-C (syn26161051). However, most of paired valids are duplicates. Best,

Created by Benxia Hu BXH
@abby.vanderlinden zcat FM_088__HiC__sample2.R1.fastq.gz | head ``` @A00297:85:HK7WMDSXX:3:1101:1362:1000 1:N:0:GACGAC NGATGTGATGTGTGGCCAGATCGATCTTAGTACACTACAGCAACAAAAGTCTTAATCAAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACGA + #FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF @A00297:85:HK7WMDSXX:3:1101:1524:1000 1:N:0:GACGAC NAAGGAGACCTCCAGACTTTTACCAGGGTAACTGTGCACTGGGGAAAGGGAAATGATCGATCATTTCAACAGCATATAAACATGTGATAGCATCTTCCAT + #FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A00297:85:HK7WMDSXX:3:1101:1561:1000 1:N:0:GACGAC NCTCGAAAAGAAGGAACATCTAAAATCAATAATCAAAGCTTTCATATTAAGCAACTAGAAAAAGAAGAGGAAATTAGATCGATCTTTGAGTGGAAAACTA ``` zcat FM_088__HiC__sample2.R2.fastq.gz | h ``` ead @A00297:85:HK7WMDSXX:3:1101:1362:1000 1:N:0:GACGAC NGATGTGATGTGTGGCCAGATCGATCTTAGTACACTACAGCAACAAAAGTCTTAATCAAGTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACGACGA + #FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF @A00297:85:HK7WMDSXX:3:1101:1524:1000 1:N:0:GACGAC NAAGGAGACCTCCAGACTTTTACCAGGGTAACTGTGCACTGGGGAAAGGGAAATGATCGATCATTTCAACAGCATATAAACATGTGATAGCATCTTCCAT + #FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A00297:85:HK7WMDSXX:3:1101:1561:1000 1:N:0:GACGAC NCTCGAAAAGAAGGAACATCTAAAATCAATAATCAAAGCTTTCATATTAAGCAACTAGAAAAAGAAGAGGAAATTAGATCGATCTTTGAGTGGAAAACTA ``` zcat FM_088__HiC__sample2.R1.fastq.gz | md5sum **9622bcfa8925a2aa79223dd86580b26a -** zcat FM_088__HiC__sample2.R2.fastq.gz | md5sum **9622bcfa8925a2aa79223dd86580b26a -** reads are totally identical
@romanko I downloaded FM_088__HiC__sample2, 3 and 4 Hi-C fastq files from synpase portal.: Here is an example: zcat FM_088__HiC__sample3.R1.fastq.gz | head -n 10 ``` @A00297:85:HK7WMDSXX:3:1101:1344:1000 1:N:0:TACAGC NTGACAGCTTAAAAGCTAGTATAATTCATCATCATCAGTTAATTTTCACTTGGTGTCCACTGGGTGCTGAACATCATACAAGGCTCTTTGTCAGCATATA + #FFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A00297:85:HK7WMDSXX:3:1101:1633:1000 1:N:0:TACAGC NAACACCAAGAATGACAGAATGGAAAGATGATCCCTATTTCCCATCTCATAACTTGTTTTAAGAAGCGCAGCATAATAATGTGTGGGCTTGGGATTCAGT + #FFFFFFFFFFFFFFFFFF:FFFFFFFFFF,F,FFF,::FFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF @A00297:85:HK7WMDSXX:3:1101:2917:1000 1:N:0:TACAGC NTGAAGAGATTTGAGCTCAGAATTTTGCAGAGTTGAAAGATACAGGCTGCTCTGCCTATGGAGTAGCCATTCTTTATTCCTTCACTTAATAAATTTACTT ``` zcat FM_088__HiC__sample3.R2.fastq.gz | head -n ``` 10 @A00297:85:HK7WMDSXX:3:1101:1344:1000 1:N:0:TACAGC NTGACAGCTTAAAAGCTAGTATAATTCATCATCATCAGTTAATTTTCACTTGGTGTCCACTGGGTGCTGAACATCATACAAGGCTCTTTGTCAGCATATA + #FFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF @A00297:85:HK7WMDSXX:3:1101:1633:1000 1:N:0:TACAGC NAACACCAAGAATGACAGAATGGAAAGATGATCCCTATTTCCCATCTCATAACTTGTTTTAAGAAGCGCAGCATAATAATGTGTGGGCTTGGGATTCAGT + #FFFFFFFFFFFFFFFFFF:FFFFFFFFFF,F,FFF,::FFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF @A00297:85:HK7WMDSXX:3:1101:2917:1000 1:N:0:TACAGC NTGAAGAGATTTGAGCTCAGAATTTTGCAGAGTTGAAAGATACAGGCTGCTCTGCCTATGGAGTAGCCATTCTTTATTCCTTCACTTAATAAATTT ``` ACTT R1 and R2 have the same sequences. That is impossible. can you please double check FM_088__HiC__sample2, 3 and 4 Hi-C fastq files?
The provided HiC data was providing high resolution results in our hands: I am linking Pengfei Dong who was processing the HiC data, and would be the best person to address the concerns @PFDong. Roman
Hi there, @romanko is the first author on this paper and he may be able to help answer your question.

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