How to retrieve reads from fasta file based on a list of identifier? name

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#1

Hello,

Is there a tool in usegalaxy that can help me retrieve reads from a fasta file (8Gb) based on a list of read identifier names (~150)? The list of identifer names is in a text file but I can convert to fasta or something else. I’d then run the selected reads through blast for ID.

Thanks for any help.

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#2

Hi @dacosta,
in order to extract a set of reads based on a list of identifiers you can use the seq_filter_by_id tool. Previously you will need to set the text file datatype as tabular.

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#3

Thank you so much for your reply @gallardoalba. I might be mistaken but it looks like I’d need to use this tool with python. Thanks in part to your reply, I was able to find the filter fasta tool which does the same thing but is an online usegalaxy tool.

#4

Yes, you can find that tool in Galaxy as Filter sequences by ID (if you look for seq_filter_by_id in the tool search bar you will get the same result).

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#5

Ahhh I see! I only searched for a portion of that keyword originally. Thanks again @gallarsoalba

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