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Question: Galaxy app to retrieve selected raw reads
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gravatar for lukacdm
2.6 years ago by
lukacdm • 0
United States
lukacdm • 0 wrote:

There are many previous threads regarding how to retrieve selected raw reads from fastq files offline; does anyone know of a public galaxy instance with a tool that can return a set of raw reads using a query of post-filtered, post-mapped reads?
fastq tool retrieve filter • 623 views
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modified 2.6 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.6 years ago by lukacdm • 0
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gravatar for Jennifer Hillman Jackson
2.6 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Convert fasta/fastq to tabular format (Convert Formats) then perform a Join between the list of sequence IDs on your file and the first column of the new tabular dataset (representing sequences). At the end convert the extracted sequences from tabular back to fasta/fastq.

Extract this protocol, once in your history, into a workflow for re-use if it is an operation that will be reused.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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