I am quite new to the whole genomics/bioinformatics field and this forum has already helped me a lot :) So I hope you can give me some hints at this problem:
We ran a first Hi-C trial and I am currently mapping the fastq files to our reference genome. I first used samtools fastq to convert the bam file to the forward and reverse fastq reads. Aligning with bowtie2 without any trimming resulted in an alignment rate of about 60%. So I thought with the HiCUP pipeline I could improve the alignment rate. I used the same bowtie2 library as before and used hicup digester to digest the ref. genome with --re1 A^AGCTT,HindIII. Then I ran hicup and it returned only 10% paired reads (30% unique alignments, 40%multiple alingnments, 30% failed to align) for both fastq files.
Does anyone have an idea where this low rate could come from? fastqc reports look ok to me and bowtie2 performed much better, even though its also not so great.
I will try Hic-pro next but it would be nice to know what happend.
Best and thanks for your help!