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Question: Select lines in Galaxy (using Select tool)
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gravatar for bodega.roberta
2.9 years ago by
bodega.roberta • 0
bodega.roberta • 0 wrote:

Hello,

I'm working with some reads in tabular format and I wish to select those who start with either one of these strings:

CTACAGGTGGTCAAGTATTTATGGT or TACAGGTGGTCAAGTATTTATGGT

The same sequence is present in other reads that I wish to discard, but in these latest they're not in the beginning of the string.

I used the "Filter and Sort"/"Select" function, matching this string

/t(CTACAGGTGGTCAAGTATTTATGGT)|(TACAGGTGGTCAAGTATTTATGGT)

but I was unsuccessful. Any suggestion?

Thank you,

Roberta

 
galaxy • 646 views
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modified 2.9 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.9 years ago by bodega.roberta • 0
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gravatar for Jennifer Hillman Jackson
2.9 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

First convert to tabular with Fasta-to-Tabular. Next use the expression below with Select. End with a convert back to fasta with Tabular-to-Fasta.

^.*\t(CTACAGGTGGTCAAGTATTTATGGT|TACAGGTGGTCAAGTATTTATGGT).*$

Thanks, Jen, Galaxy team

 
ADD COMMENT • link written 2.9 years ago by Jennifer Hillman Jackson ♦ 25k

Thanks! It was very helpful.

Best,

Roberta

 

ADD REPLY • link written 2.9 years ago by bodega.roberta • 0
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