Hello, I have performed htseq on my BAM files, where I got very high number of no_feature. I have tried using name sorted BAM file …

Hello, I am doing RNAseq analysis, i got above 90% alignment score in mapping step using HISAT2, but when i am trying to do quantification …

I am trying to generate a count table after aligning my CLIP-seq results to a genome index. I have been using several online tutorials, but …

Hello, I have 15 BAM files, with 5 belonging to each of the control, treatment1, and treatment2 groups. I am wondering whether I should use …

Hello, I have a RNAseq dataset -BAM files from chimps and a BED file with chromosome- coordinates for sequences of interest, I am looking for …

I am transforming sam files to bam, to facilitate their ordering I use this command, % cd /Volumes/GENOMA/BWA % samtools sort -n -O V350019555_L03_B5GHUMqcnrRAABA-551.sam | …

Hello everyone, I have some ATACseq bam files and a reference peak set(genomic regions) in text format. I am trying to get count matrix from …

Hello all, I want to sort my bam by queryname so i used the command: Samtools sort -n -m 1 -@ 10 -o /Path/ouput.bam /path/input.bam …

Hello I encountered something strange. When I use: samtools index sample.bam I see no output, error message, or new file. Then I tried it w/o …

Dear All, I have multiple name-sorted BAM files generated from pair-end DNA sequences which look like: `R1-1.bam`, `R1-2.bam`, ..., `R2-1.bam`, `R2-2.bam`, ..., and I am …