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Hi, could you please explain why we need a reduced reference genome?
Is it not possible to map the 4C to the whole reference genome and then proceed?
Also, at your bowtie2 command you trim the firs…
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I'm getting the error shown below. The proximal cause seems to be that hic_exp.py populates the dictionary dict_fragments from a file in the main output directory named "list_contig_names.txt". The re…
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Hello there I am running into an issue while running the human genome on the test file below. After I do the genome prep I see these messages. I verified that the bt2l files exist and when running ls …
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Hi.
I am trying to use your software. Once the virtualization with docker has been initialized in the readMapping function it gives me an error as if bowtie was not installed. The same is also true…
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The command that I am using:
```
perl GFusion.pl.txt -o output1 -r 0 -p 12 -i /mnt/home/soft/human/data/hg38_illumina/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/genome -g /mnt/home/soft/human…
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Using cmake results in bowtie-*-l and bowtie-*-s in being identical files.
Using the makefile to build the binaries results in different binaries for -l and -s files.
Tested in the case of both v2.5…
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Hi,
I'm running the SpliceSeq locally to process my own RNA-seq data. But I get an error "Error parsing Bowtie output file"
My SpliceSeq version is 2.1, the bowtie version is 0.12.9, the java versio…
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Dear
I am trying to do allelic analysis Hic data getting same error G2 is mapping reads are zero and iced normalisation step getting error. I used bellow command to run analysis. non allelic analysi…
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Hello! l installed hic-pro by conda , but the step "Pairing of R1 and R2 tags ..." is always wrong, can you tell me how to solve this problem?
Thank you！
**the log**
Run HiC-Pro 3.1.0
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