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LSB Version: :core-4.1-amd64:core-4.1-noarch:cxx-4.1-amd64:cxx-4.1-noarch:desktop-4.1-amd64:desktop-4.1-noarch:languages-4.1-amd64:languages-4.1-noarch:printing-4.1-amd64:printing-4.1-noarch
Distribu…
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Hi, recently I try to use your algorithm in data from https://glioblastoma.alleninstitute.org/, but bug occur, may get your help in debugging it?
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I have some bams that are corrupted and I am able to use `bamrescue` to determine that there are corrupted blocks.
However, it would be nice if `bamrescue check` set the unix return code to somet…
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Hello,
I am currently trying to call SNPs to generate an alternative fasta sequence. Whenever I combine BAM files using bcftools mpileup (bcftools version 1.20) everything runs properly until I tr…
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Hi,
I'm working with the wheat genome which has very large chromosomes, exceeding the apparent limit of 536870912.
I had to use a csi index to index the bam file (samtools index -c).
> genome_f…
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It would be useful to have a function that takes one or a set of bam files (modBam) and generates an quarto(Rmd/litedown)/html quality report (similar to the `einprot` reports).
It could be based o…
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As mentioned in comments on #698, the issue can arise if the input step already yields an indexed file. There's no reason for us to run the indexer again when the input is already indexed, so really …
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The workflow supports BAM, but the Docker wrapper was never updated to reflect that.
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Hi,
I'm using disambiguate, the C version (I used conda to install ngs_disambiguate). I have mapped (using STAR) against Human and Mouse reference genomes. After that I name sorted the bam files an…
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Hi,
Thanks for developing a subset-bam software. I would like to split the BAM file (from cell ranger) for each individual cell barcode, which is provided in the filtered_feature matrix folder (bar…