SAMtools view-BEDtools bamtoFastq
This app uses SAMtools view to filter either mapped or unmapped reads from a BAM file. Then BEDtools bamtofastq is used to convert the remaining reads to a fastq file.
- To use SAMtools view-BEDtools bamtoFastq import your data in BAM format.
- Resources: https://github.com/arq5x/bedtools2, http://www.htslib.org/doc/samtools-1.7.html
Use TrmPr1_frag_1.fastq.bam from the directory above as test input.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Default parameters only, no further configuration needed.
Expect a fastq files named as set in the output.