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Dear team,
I am trying to run the ATAC seq pipeline but it encounters and error and exits in the first few minutes. My JSON file is correct and the genome.tsv URL is also correct, I have checked mu…
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Hello,
I ran the test data in the login node of HPC cluster:
```
nextflow run /public/home/zyqi/pan-TE-analysis/GraffiTE/GraffiTE/main.nf \
--assemblies assemblies.csv \
--TE_library huma…
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Hi, dear friends. I have a question on processing rawdata. When I made PCA or Dst. analyses, I need to take a outgroup species as reference genome for processing rawdata. My question is that whether t…
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Hi,
What is your suggestion to extract the representative genome for a meta_ and ext_ mOTUs?
E.g., if we download meta_mOTU_v3_12240, it downloads 4361 genomes (even if we only choose one of th…
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Thanks for the good material. I have a question about the alignment using bowtie2, here according to [`mutation_sequencing_analysis_script.sh`](https://github.com/aldob/iMUT-seq/blob/4476db76f2058d0af…
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Hi,
The estimated genome size of the coastal redwood output by GenomeScope is 27.0 Gbp and 2.293 Gbp for Gossypium barbadense in this paper . But I'm confused about how to get these results from http…
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Hello,
When attempting to run lumpy on NA12878 processing stops and it appears as though a core dump occurs.
Any suggestions?
samtools view -f 97 -F 28 /analysis/projects/myseq/gatk/v4/NA12878/bam//…
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I get the below error when running on a HPC with 120 cores and 500GB RAM. I read that 137 relates to memory so I increased the allocation to 250G using the -c parameter and a mem.config file, as sugge…
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Hi,
I'm trying to generate a library from scratch based on GRCh38 with some regions masked (GRC exclusions). Very early in the main script, the reference genome FASTA is copied to a file with the m…
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This issue contains monthly updates to an automatically ranked list of PubMed papers as candidates for curation in the Bioregistry. Papers may be relevant in at least three ways:
(1) as a new prefix…