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Question: Convert multiple FASTQ files into one BAM file
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gravatar for angelkyril
9 weeks ago by
angelkyril • 0
angelkyril • 0 wrote:

Hello guys! I recently started working with NGS analysis and I may have a stupid question to ask.

Through lab analysis (nextseq 500 Illumina) using paired-end sequencing, I produce 8 fastq files, 4 forward and 4 reverse from the same sample. Ideally the 4 forward should be identical as well as the 4 reverse files (but they never are).

I want to convert the 8 FASTQ files into 1 BAM file. What is the procedure I need to follow using galaxy tools? I imagine that the 4 forward files should somehow become 1 file. Should I use the concatenate tool?

Thank you very much in advance!! Please save me!
galaxy bam • 116 views
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modified 9 weeks ago by Jennifer Hillman Jackson ♦ 25k • written 9 weeks ago by angelkyril • 0
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gravatar for Jennifer Hillman Jackson
9 weeks ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Technical replicates provide informative metrics. Please see the Galaxy tutorials for details: https://galaxyproject.org/learn/

  • Start here: NGS logistics - this is an introduction to Galaxy's functionality for the analysis of Next Generation Sequencing data. https://galaxyproject.org/tutorials/ngs
  • Then review tutorials that cover your analysis objective for more details. How to structure the post-QC/QA data for an analysis workflow can vary.
  • Directly merging technical replicate data at the fastq level (with concatenate) would never be recommended.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 9 weeks ago by Jennifer Hillman Jackson ♦ 25k
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