Question: How to convert unaligned reads to Fastq format after initial alignment?
gravatar for chalagarciad
21 months ago by
chalagarciad0 wrote:

I aligned my sample against human chromosome 19. Now I want to use the unaligned reads and align them against a virus genome.

Is there a way to convert the unaligned reads into fastq format on Galaxy? or is there another software that would allow me to do this?

I appreciate any help!

alignment bowtie • 1.0k views
ADD COMMENTlink modified 21 months ago by Guy Reeves1.0k • written 21 months ago by chalagarciad0
gravatar for Guy Reeves
21 months ago by
Guy Reeves1.0k
Guy Reeves1.0k wrote:

If you are using bowtie for mapping you can activate this option 'Write unaligned reads (in fastq format) to separate file(s) ' . This is one of the mapping programme that can do this as Jen says

ADD COMMENTlink written 21 months ago by Guy Reeves1.0k
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k wrote:


This is how:

  1. Sort the output BAM/SAM dataset from mapping
  2. NGS: SAMtools > Sort BAM dataset using the option to sort by chromosome
  3. Other options:
  4. Filter the BAM/SAM output for unmapped reads
  5. NGS: SAMtools > Filter SAM or BAM, output SAM or BAM using the option under "Filter on bitwise flag"
  6. Extract the fastq reads
  7. NGS: Picard > SamToFastq

Some mapping tools have an option to output a BAM of only unmapped reads at run time. If you use this, the second item (filtering the primary mapping output BAM/SAM) can be skipped. For example, Tophat > TopHat settings to use > Full Parameter list > Output unmapped reads set to "Yes".

Thanks! Jen, Galaxy team

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k
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