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We would like to reduce memory consumption during population calling. Is it possible to split SNF files by chromosome or genomic region?
Alternatively, should we supply smaller bams to Sniffles2…
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gridss conda installation
jar file 2.13.2-gridss-jar-with-dependencies.jar
platform : Ubuntu 22
The code I ran
`gridss -t 20 -r ./reference/Ref/GRCh38.p14.genome.fa -j ~/tools/gridss-2.13.2-gri…
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The index used (1000) can be modified in Options, but if you're working on several images, updating that all the time is unwieldy. Plus, if it creates more than one page, the tactic may fail.
So I …
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Hello, I'm attempting to convert the HG001 BAM files to FASTQ format for benchmarking purposes. However, I'm facing challenges aligning the generated FASTQ files to my reference genome. Could you prov…
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Dear administrator.
Hello, this error occurred when I was using juicer to process HIC data. How should I solve this problem?
The error is:
[bam_sort_core] merging from 1530 files and 170 in-memor…
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Hello,
I am using popscle dsc-pileup function as a prelude for running demuxlet on cellranger output. Here is my code:
`packages/popscle/bin/popscle dsc-pileup --sam bam.bam --vcf vcf1.vcf --out h…
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```python
data_processor.generate_training_sample(data_mode, sample_list_file, bin_size, proportion)
# data_mode: Smart_seq
# bin_size: 5
# proportion: 80
```
When I analyzed smart-seq data …
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How could I run QoRTs on multiple bam files in the java command line? It seems only one sample is accepted in the java command line.
Would be possible to make something like following work? or give a…
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Hi,
I need some help.
Can I use bcftools mpileup for creating vcf file from bam files ? Or do I need to run germline caller like GATK or GATK CNV caller. I have WGS bam files.
Also, my vcf…
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Hello!
I'm having difficulty running the program in a stepwise fashion:
After copying two bam files to lscratch, I receive the following error:
"Exit: Error: Directory Hierarchy of rawdata '/lscr…