Question: Can't filter unmapped reads in my BAM file
gravatar for ad00fernandes
18 days ago by
ad00fernandes0 wrote:

Hello everyone. I'm a newbie in bioinformatics and I'm trying to filter a BAM file using the Galaxy platform. Thing is, all I want are the unmapped reads, but I can only find the option to select mapped reads. Additionaly, while trying to run some tests, I have converted this file to the FASTA format to run a local BLAST (due to the huge size of it) and I've been having issues with the program stating that my queries are "not accessible". Maybe is that a problem with the conversion? I know this may sound foolish but I'll be grateful if someone could help me.

fastq rna-seq galaxy filter bam • 40 views
ADD COMMENTlink modified 16 days ago by Jennifer Hillman Jackson25k • written 18 days ago by ad00fernandes0
gravatar for Jennifer Hillman Jackson
16 days ago by
United States
Jennifer Hillman Jackson25k wrote:


These tools can filter for unmapped reads directly:

  • NGS: SAMtools > Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region
  • NGS: Picard > FilterSamReads include or exclude aligned and unaligned reads and read lists
  • NGS: Peak Calling > BAM filter Removes reads from a BAM file based on criteria

And this one can have a query constructed that will exclude/include multiple bitwise flags in more complex ways:

  • NGS: BamTools > Filter BAM datasets on a variety of attributes

To convert SAM/BAM to fastq/fasta, try these:

  • NGS: BamTools > Convert, Merge, Randomize BAM datasets and perform other transformations
  • NGS: Picard > SamToFastq extract reads and qualities from SAM/BAM dataset and convert to fastq

If you think a tool may have a bug (doesn't create a valid fasta dataset), please send in a bug report and we will review.


  • My job ended with an error. What can I do?
  • Reporting Usage Issues or Software bugs

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 16 days ago • written 16 days ago by Jennifer Hillman Jackson25k
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