Hi, I know Bowtie1 in Galaxy have the option --un to write in a separate fastq file all non mapped reads. But where is the option to write in a fastq file all reads that are mapping (--al)? I need it as I want to work further with these reads that do not map.
It looks like there was a typo.. do you mean "To work with the reads that do map"? (Since the output already provides the unmapped fastq reads).
There are two options:
- Stick with Bowtie for Illumina (Bowtie v1.x) - only has the unmapped fastq option implemented
- Use Bowtie 2 instead - the output mapped fastq option is included on the tool form, near the option to output unmapped
If you choose to stay with Bowtie v1, below is how to get the mapped fastq reads (there are other ways, but this method is simple/short):
- Sort the SAM file with the tool NGS: Picard > SortSam.
- Filter the SAM dataset to include only mapped reads. Use the tool NGS: Samtools > Filter SAM or BAM, output SAM or BAM. Use the option Filter on bitwise flag as yes to expand the form to set the filter criteria (Mapped + whatever else you may wish to filter on).
- Extract the fastq sequences from the sorted, filtered SAM dataset. Use the tool NGS: Picard > SamToFastq.
Hopefully this helps! Jen, Galaxy team