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• remove a percent of reads from a BAM file
  I would like to remove x% of reads from a BAM file at a specific region . For instance : remove ...
• remove low number of reads from BAM file
  Dear All, I want to remove low number of reads from alignment BAM file. How can I do that?
• How Can I Extract All The Read Pairs In A Region From Bam File ?
  how can I extract all the read pairs that one of the read in a region from BAM file ?
• Removing Pcr Duplicates From Bam Without Collapsing Sequences By Position?
  Is there a tool that removes PCR duplicates from a BAM file if they are above the background leve...
• How to efficiently remove a list of reads from BAM file?
  Hi Guys, I have a BAM file, and a big read list. What I want to do is to remove the reads in the...
• Remove reads counts overlapping with blacklist regions in BAM files
  Hi all, I am preprocessing some bam files for differential binding analysis. I have read that s...
• Removing the OQ tag from a BAM file
  Hello, I'd like to remove a tag (not a read) from a BAM file.  I would like to remove the OQ tag...
• Isolating reads from specific region from bam file
  I have RNA-seq data and would like to get the reads from specific region for example -/+ 50 reads...
• How do I filter a BAM file for proper pairs WITHOUT samtools
  I need to remove unpaired reads from my BAM file... and I'm looking for a non-samtools way of doi...
• How to remove specifically non aligned regions
  Hi all, I would like to select a specific region from a fastq file (all read matching this regio...
• Is there a correct order in which to filter BAM files?
  Say I have a BAM file which I want to filter, I want to apply the following processing steps: Rem...
• extracting mapped reads from the bam file
  Hello all, I am trying to extract the mapped reads from a bam file for a specific region. sam...
• Extract reads where both pairs maps properly and none of the pairs are split from a bam file
  Hi, I want to extract only those reads from bam file in a given region where both pairs are mapp...
• Remove some reads from a BAM file
  Hi, I have a paired-end BAM file and I found that some pairs/mates have identical positions on t...
• Samtools flagstat unpaired reads
  Trying to quickly remove reads samtools flagstat deems as unpaired from BAM file? Thanks.
• Remove Intronic Regions in .BAM
  Hi I have a .BAM file which contains discordantly and concordantly mapped mate-pairs. I used bed...
• Should I Remove The Unmapped Reads From My Bam ?
  is it a good practice to remove all the unmapped reads with: samtools view -F 4 after they've ...
• fgbio: Calling consensus reads using UMI
  Hi, I'm struggling a little bit with some data containing UMIs. It's enriched DNA-seq on specifi...
• Removing CDS from my bam file plot
  Hello everyone, I just plotted my bam file by using GenomeAxisTrack(),IdeogramTrack(),GeneRegion...
• Removing Human Reads From Metagenome BAM File
  So I have metagenome bam files which contain reads for both human and bacteria. I would like to r...
• Removing Duplicate Reads Post Alignment
  Hi, I'm analyzing RNA-Seq data and I want to check for snp in it. For that, I want to remove dup...
• how to find the amplified region from aln.bam file
  I have received mi-seq data for targeted genomic region of human. I need to find the amplified re...
• Extract parts of reads from BAM file that overlap a specific region of genome
  Assuming that I have a BAM file with aligned reads, how can I extract the part of all reads that ...