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I'm trying to convert a 19gb .sam file to .bam format using the samtools view command. I've seen a related [issue thread](https://github.com/samtools/samtools/issues/67) on this site where it was sta…
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Hello, I am using BRAKER for the first time to annotate the genome of a plant with an approximate genome of 3Gbp. I have RNA-seq data and a fasta file of proteins from a plant of the same species and …
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Hi, I know that there is a section which says that BAM file should be used from BWA MEM, but does this mean that we could also use BAM file created by GATK best practice workflow, which means that BAM…
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**[Original report](https://bitbucket.org/whatshap/whatshap/issue/217) by Milad Mortazavi (Bitbucket: [Milad Mortazavi](https://bitbucket.org/Milad Mortazavi), ).**
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```
This functionality should exist. Just haven't had time to add it yet.
```
Original issue reported on code.google.com by `aaronqui...@gmail.com` on 17 Jul 2010 at 12:31
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Hello, I'm a graduated student studying bioinformatics in South Korea.
I'm trying to do detect extrachromosomal DNA (ecDNA) in nanopore long-read targeted sequencing data.
I followed the workflow …
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Hi all,
I'm working on an HPC, and the automatic installation of plugins fails:
```
nf-test test main.nf.test --profile singularity
🚀 nf-test 0.8.4
https://code.askimed.com/nf-test
(c) 202…
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Hi all,
i have a bit of a problem when using a modified approach of aligning my Hi-C data with the bwa-mem algorithm.
I'm using HiCExplorer version 3.7.2 and python 3.8.0
When aligning the pa…
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### Subject of the issue
The docker container for the jvarkit software (https://hub.docker.com/r/lindenb/jvarkit) is throwing a memory error:
"There is insufficient memory for the Java Runtime Envi…
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Hi Wouter,
would there be a possibility of including multiple input file types (eg for 1 sample to include both the sequencing summary file (--summary) and bam (--bam) file), instead of running the…