-
Querying human reads to the human genome ([ref](ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_genomic.fna.gz)) is very slow (~500 RPM, a **1000x…
-
I ran rnabloom on several of my input files individually. out of my 10 samples, it did not produce any transcriptome file for 2 of them. Why is that? It finished running but there are no output files.…
-
Hi,
Thank you for developing HapHiC, it exhibits excellent performance in polyploid scaffolding. I have two questions and hope you can provide assistance:
Q1: How does HapHiC process collapsed conti…
-
Hi,
I was trying to build the spliceu index for the ensembl rat genome.
I used conda to install simpleaf
`mamba create -n af -y -c bioconda -c conda-forge simpleaf piscem`
Then I downloaded unzi…
-
Hi,
I've been playing around with a dataset of a bird we have where we have HiFi, Hi-C and ONT reads. I get a seg fault with this assertion failing:
`hifiasm: gfa_ut.cpp:2303: void filter_sg_by_ug(a…
-
Hello,
I'm using trycycler to assembly a bacterial genome with pacbio data, for generating assembly I modified the ```miniasm_and_minipolish.sh``` script to adress the reads type (```minimap2 -x ava-…
fetyj updated
2 months ago
-
Hello @zengxiaofei ,
I used hifiasm with hifi and HiC data, and generate haplotype-specific data, including p_ctg.fa, p_utg.fa, r_utg.fa, and hap*.p_ctg.fa.
As you mentioned in the tutorial, if I wa…
-
When I provide a plink file with unitig positions in the 3rd column, the colours in the 5th column are not displayed (all points are grey and sized corresponding to the length). If I use the same file…
-
**Q:**
Haphic is very convenient for processing Hi-C data.
We combined the data of two haps together and then processed it with haphic. The resulting Hi-C heatmap shows some strong interactions bet…
-
Hello, I got this error:
```python
Error: Error detecting input file format. First line seems to be blank.
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File …