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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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"Forward and reverse reads not paired. Check that BAM files have the same read names and are sorted." #633

Open panapapa14 opened 1 month ago

panapapa14 commented 1 month ago

Hello there! I am facing the problem I am writing above. I have read plenty of related online comments and I have figured out that my BAM files were not sorted. My difficulty lies in the fact that I use the docker image and I am not sure how I am supposed to continue the execution after manually correcting the initially non-sorted BAM files. I have already tried to use the R1 and R2 bwt2merged.bam files (instead of the initial fastq files) in combination with the following command:

sudo docker exec -it hicpro3.0 /HiC-Pro_3.0.0/bin/HiC-Pro -i /HiC-Pro_3.0.0/transfers/rawdata -o HiC-Pro_3.0.0/transfers/output -c /HiC-Pro_3.0.0/transfers/config-hicpro.txt -s proc_hic -s merge_persample -s build_contact_maps -s ice_norm

but weirdly I get the very same error in my log files.

panapapa14 commented 1 month ago

Any ideas..?

nservant commented 1 month ago

Hi, If you are using -s proc_hic, the input parameter (-i) has to be updated to get the bam files after mapping. Of note, I would suggest to look now at the nf-core-hic pipeline which can be seen as a Nextflow version of HiC-Pro and is much more flexible to resume a pipeline or to play with the CPU/RAM requirement.

https://nf-co.re/hic/2.1.0/docs/usage

panapapa14 commented 1 month ago

Hello! Thanks for the comment about nf-core-hic, I found the information about it very well organized and useful! I have a question about the pipeline though. When I try to use unzipped fastq files as input in my .csv file, I got an error telling that I must use fastq.gz files. But when I use the zipped versions of my samples I observe that the FASTQC step doesn't have access to my files and the process is being killed. Any suggestions?