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.
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