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Hi，
In Filtering SAM file step : PreprocessSAMs.pl sample.bwa_aln.sam draft.asm.fasta MBOI; you use MBOI enzyme.
but in Partition step : ALLHiC_partition -b prunning.bam -r draft.asm.fasta -e AAGCTT…
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hi,I can't invite the host 59.79.232.12,can you give me a favor.here is my method:
I used the filezilla to connect the host.I set the host as ftp://59.79.232.12/ and username as AllHiCData and passwo…
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Hi,
I would like to test all-hic and am stuck at the pruning step using the command:
```
ALLHiC/scripts/prune.pl -i Allele.ctg.table -b bam.files.txt -r Simon_Salmon.flye15K_pilon.fasta
```
…
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Dear community,
I understand the input of original draft assembly for ALLHic scaffolding is contig-level. I am curious that is it possible to use scaffold-level assembly as input data? I have one d…
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Hi,
I try to create allele.ctg.table files but run into trouble running the classify step.
classify.pl returns following errors:
```
Use of uninitialized value $tgene in substitution (s//…
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Hello,
Thanks for this great Hic pipeline. A month ago, I had some trouble of the spending too much time for "Optimize" steps. And you suggested to check the data format, command lines and log file w…
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Hi,
Thanks for sharing this program. I was trying to use ALLHiC to help with my genome assembly, however, the first step `Map Hi-C reads to draft assembly` ran almost one week and still not finished…
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Hi,
I have a fresh highly polymorphic denovo assembly and I am not planning on doing annotation before I phase the genome. Is there a way to create Allele.ctg.table without annotation (CDS and GFF3…
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Could you please elaborate on the format of the user-prepared.clusters.txt file to carry out the globally rescue step?
thanks,
Diego
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Hello,
Thanks for this great Hic pipeline. I have some trouble of the spending too much time for "Optimize" steps. My target genome is about 500 MB, and 11 chromosomes. But first I just tried K=16 to…