Tag: samtool

Extracting chimeric reads from mapping

Hello, I am struggling to processing and analyse bam files (from bwa alignment), to extracting the chimeric read alignment. I am aligning human cell line RNA-seq data (paired end) to virus, aimed to find the viral integration sites in the genome. For that, after reading a bit here from following…

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Calculating Average Coverage or Read Depth for a Sequence (WES)

Calculating Average Coverage or Read Depth for a Sequence (WES) 0 Hi, I might as well ask this community as well just to be certain Background: I mapped my reads to reference genome, then used SAM tool flagstat and SAM tool stats. Felt like using both but at the same…

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failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels:

Solving environment: failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels: 1 I am trying to install samtools on my environment bioconda with this command: bioconda install samtool I get this error: Solving environment: failed with initial frozen solve. Retrying…

Continue Reading failed with initial frozen solve. Retrying with flexible solve. PackagesNotFoundError: The following packages are not available from current channels:

Chipseq data peak calling issue

Hi , I’m trying to do analysis of chipseq data . I have 3 samples Sample1 , sample2 and input I have done QC and then alignment using Bowtie . After that I used samtool to get bam files . Then I have used Picard for duplicate removal. Now I…

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Problem generating a .vcf after upgrade of samtools and bcftools

Problem generating a .vcf after upgrade of samtools and bcftools 1 Hi I used to go over candidate sites of variation using SAMtools mpileup after which I used to execute some evaluations of the data using BCFtools. In general I used to provide the reference fasta genome and use the…

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Filteration of uniquely mapped reads

Filteration of uniquely mapped reads 2 Hello I have BAM-full file with reads mapped to “human and mouse” chromosome file. Now I would like to extract reads mapped only to “mouse” (means not mapped to human chromosome”. This is the protocol I am using : From BAM-full, extract reads mapped…

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[SOLVED] changing the order of input changes samtools merge ouput

I realized that this is a stupid mistake I have made. Since samtools do not overwrite the files by default, the output that I get from samtools merge output.bam f2.bam f1.bam wan’t what I thought it was below is my original post ++++++++++++++++++++++++++ I’m using samtool/1.9.0 and I’m trying to…

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Disappearing CB, the bam tag after samtools sort -t CB

  I’ve been trying to setup an analysis pipline for RNAvelocity in AWS EC2. I used one of the 10x dataset, 10k Peripheral blood mononuclear cells (PBMCs) from a healthy donor, Single Indexed, as a test model to setup the pipeline. For speed and cost saving, I first used samtools…

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