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Question: How to convert unaligned reads to Fastq format after initial alignment?
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gravatar for chalagarciad
21 months ago by
chalagarciad • 0
chalagarciad • 0 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
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modified 21 months ago by Guy Reeves • 1.0k • written 21 months ago by chalagarciad • 0
1
gravatar for Guy Reeves
21 months ago by
Guy Reeves • 1.0k
Germany
Guy Reeves • 1.0k 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 COMMENT • link written 21 months ago by Guy Reeves • 1.0k
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gravatar for Jennifer Hillman Jackson
21 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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: https://github.com/jennaj/support-prior-qa/wiki/Sort-your-inputs
  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 COMMENT • link written 21 months ago by Jennifer Hillman Jackson ♦ 25k
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