Tag: cram

Provided by: biobambam2_2.0.179+ds-1_amd64 NAME bamfillquery – fill query sequences into BAM files SYNOPSIS bamfillquery [options] <in.bam queries.fasta >out.bam DESCRIPTION bamfillquery reads a SAM/BAM/CRAM file and a FastA file, copies the sequences found in the FastA file into the query sequence field of the SAM/BAM/CRAM file and writes the resulting data…

Cloneable is not used very much so maybe deprecate and remove the clone() method? /cc @jmthibault79, @cmnbroad See spotbugs.readthedocs.io/en/stable/bugDescriptions.html#cn-class-defines-clone-but-doesn-t-implement-cloneable-cn-implements-clone-but-not-cloneable Part of #1267 Report: In class htsjdk.samtools.cram.structure.CramHeader In method htsjdk.samtools.cram.structure.CramHeader.clone() At CramHeader.java:[lines 80-85] Read more here: Source link

I’m using RStudio on Ubuntu 18 and I’m trying to install the htslib package from the Bioconductor repo, but I’m stuck now. This is what I get: * installing *source* package ‘Rhtslib’ … ** using non-staged installation via StagedInstall field ** libs cd “htslib-1.7” && make -f “/usr/lib/R/etc/Makeconf” -f “Makefile.Rhtslib”…

Hi all, We store our alignment files on aws s3. I would like to be able to open them with IGV without needing to download them completely, but I can’t find an optimal solution. If I get a pre-signed url it works but it’s not convenient. I try to follow…

Provided by: samtools_1.13-2_amd64 NAME samtools reheader – replaces the header in the input file SYNOPSIS samtools reheader [-iP] [-c CMD | in.header.sam ] in.bam DESCRIPTION Replace the header in in.bam with the header in in.header.sam. This command is much faster than replacing the header with a BAM→SAM→BAM conversion. By default…

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Bedtools: Merging Many Bed Files 2 I am using the algorithm CookHLA for my research. As part of its preparation, I need to feed it a bed file representing at least 100 of my samples. I have made the bed files for 500 samples using samtools and bedtools in a…

Best Omic file compressor? 1 Our team has been having storage space issues; we predicted that we will not have enough available memory to store the files generated by our pipelines. Standard file compressors (gzip, bzip2, 7zip) weren’t cutting it and I started experimenting with file-specific compressors. This is where…

[main_samview] fail to read the header from “-“. 1 I am attempting to run a file through an algorithm I have been using, HLA*LA. On running the samtools command within the algorithm, I have unfortunately been getting this error. After trying to debug this following other guides, I am seeking…

How to extract all sequences mapped to a transcript from Kallisto output 0 I ran Kallisto with the –pseudobam option. How do I extract all the short reads that are mapped to a single transcript (e.g. ENST00000367969.8)? As a person without any previous SAM/BAM experience, I tried the following things…

install GenomicFeatures fail 1 @5b9023e7 Last seen 19 hours ago China BiocManager::install(‘GenomicFeatures’) results show ‘getOption(“repos”)’ replaces Bioconductor standard repositories, see ‘?repositories’ for details replacement repositories: CRAN: mirrors.tuna.tsinghua.edu.cn/CRAN/ Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.0 (2021-05-18) Installing package(s) ‘GenomicFeatures’ also installing the dependencies ‘Rhtslib’, ‘Rsamtools’, ‘GenomicAlignments’, ‘rtracklayer’ Packages which are only…

BAM compression: .tar.gz = same size as before? 2 I tried to compress 5 bam files using: tar -czvf original_bams.tar.gz *.bam The resulting file sizes (“ll –block-size=M”) are: 8067M file1.bam 6962M file2.bam 10662M file3.bam 7794M file4.bam 7346M file5.bam 40828M original_bams.tar.gz There’s a difference of 3MB between the archive and the…