Hello,
thanks for sharing thes great resource in microglia. I followed the author's pipeline to analyze microglial Hi-C (syn26161051). However, the quality of these Hi-C is not good, most of paired valids are duplicates. I am just wonder whether the authors also got the similar results.
Best,
Created by Benxia Hu BXH @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
NTGAAGAGATTTGAGCTCAGAATTTTGCAGAGTTGAAAGATACAGGCTGCTCTGCCTATGGAGTAGCCATTCTTTATTCCTTCACTTAATAAATTTACTT
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.