Tag: samtool
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…
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…
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…
[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…
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…
