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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Low Read Alignment in Initial Bowtie Step #626

Open IzaakH-A1 opened 3 months ago

IzaakH-A1 commented 3 months ago

Hi, I seem to be getting really low initial alignment from Bowtie from my Hi-C data.

I made the bowtie mm10 index from the downloaded UCSC .fa file and then used the same file to generate the digest bam file for MboI.

I want to ensure I am doing everything right before I contact the sequencing company.

I have attached my config file - can anyone see any errors in here that may be causing a problem.

config-hicpro_FINAL.txt

Screenshot 2024-03-15 at 13 35 59

Sample_1_LogFiles.zip

Thank you

Qikiiso commented 1 month ago

Hi, I'm having the same problem as you and would like to ask if you found the cause of this problem and what should be done to fix it.

Thank you