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• How to remove duplicate sequence
  Our Ribo-seq libraries involved a PCR step (9 cycles of amplification) in order to get enough mat...
• RNA-seq data to check impact of PCR duplicates
  I have aligned my reads using HISAT, filtered and merged my data into a BAM file. I have tried re...
• Problems with MACS peak calling--FDRs of 100%
  Hello, I am having some issues with MACS peak calling. I have 5 files in my ChIP-Seq dataset (in...
• Remove PCR duplicates through Unique Molecular Identifiers (UMIs)
  Dear all is there a specific tool in Galaxy to correctly remove PCR duplicates from alignment fil...
• Chip-Seq Normalization To Total Number Of Reads
  Dear Galaxy, I am trying to analyze my ChIP-Seq data from Illumina using Galaxy. I have 2 datase...
• Do I need to normalize the ChIP-seq BAM files before run MACS?
  Hi Everyone, The experimental ChIP-seq datasets I am analysing have two times of aligned reads t...
• Quality metrics of ChIP-seq BAM files??
  Hi all, I'm a real beginner in the field of ChIP-seq analysis and bioinformatics in general (so ...
• Removal Of Duplicates And Cufflinks Usage
  Hi All I've started analyzing my RNA-Seq data for two time points: Day0 and Day4 for control an...
• removing of duplication in RNA seq
  Hi I am new in bioinformatics and in Galaxy too so please bear with me Soon I will have RNA seq...
• Trimmomatic Input Values
  Hello- I am using Trimmomatic to improve the quality of my RNA-seq data. I am using the followi...
• Help with genomics courese question
  Hello Biostar members, I am currently taking a course and we have some homework in which we need ...
• Error message: This job was terminated because it used more memory than it was allocated
  Hi,  I'm processing exome data (enriched with Nextera kit) in Galaxy. After mapping the reads us...
• Reads on Y chromosome while doing sequecing with a female donor
  Hello, When looking closely to my alignments data I found something interesting. Some of my read...
• Duplicate Reads
  Dear all, When is it necessary to remove duplicate reads from your RNA Seq analysis? Is it requi...
• Whole Exome Sequencing
  I recently got on a project that is attempting to find novel mutations in certain diseases by com...
• ChIP-seq sequence data sources
  hi I predict nucleosome using the chip-seq. i need to chip-seq data (bovine) . please tell me ho...
• Visualizing BigWig is UCSC genome browser: link not available
  I wish to visualize some bigwig files generated from bamCoverage tools in the UCSC genome browser...
• How to know if mapping to reference genome was succesful?
  Given a set of BAM files for single-end reads just mapped with BWA tool, how can I have an overvi...
• Macs- Duplicate Reads Removal
  Hi, Does MACS remove duplicate reads automatically during the peak calling? I'm running controls...
• An odd number of differential peaks in MACS2
  hi, I'm working with ChIP-seq data and using MACS2 version- macs2 2.1.0.20140616. I run MACS2 c...
• Alternative To Fpkm From Cufflinks
  Hi all, Is there any way to find out the number of reads aligning to a transcript rather than the...