Galaxy Fasta Tool

Question: Galaxy Fasta Tool - Bug

8.2 years ago by

Dear Galaxy I found a bug in extracting FATSA sequence tool in galaxy. I extracted sequence of this location chr10 123229360 123229525 fgfr2 0 - GAATACTTGGACCTCAGCCAACCTCTCGAACAGTATTCACCTAGTTACCC TGACACAAGAAGTTCTTGTTCTTCAGGAGATGATTCTGTTTTTTCTCCAG ACCCCATGCCTTACGAACCATGCCTTCCTCAGTATCCACACATAAACGGC AGTGTTAAAACATGA And I checked back in UCSC browser by pasting the same location. The sequences are completely different (hg18). Could you please help me in this issue Thanx Gireesh

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modified 8.2 years ago by Hotz, Hans-Rudolf • 1.8k • written 8.2 years ago by gireesh bogu • 40

8.2 years ago by

John McPherson • 10

John McPherson • 10 wrote:

I think that you have extracted the "+" strand for your comparison. Below is the "-" strand from UCSC hg18 TTCATGTTTTAACACTGCCGTTTATGTGTGGATACTGAGGAAGGCATGGT TCGTAAGGCATGGGGTCTGGAGAAAAAACAGAATCATCTCCTGAAGAACA AGAACTTCTTGTGTCAGGGTAACTAGGTGAATACTGTTCGAGAGGTTGGC TGAGGTCCAAGTATTC GAATACTTGGACCTCAGCCAACCTCTCGAACAGTATTCACCTAGTTACCC TGACACAAGAAGTTCTTGTTCTTCAGGAGATGATTCTGTTTTTTCTCCAG ACCCCATGCCTTACGAACCATGCCTTCCTCAGTATCCACACATAAACGGC AGTGTTAAAACATGAA Dear Galaxy I found a bug in extracting FATSA sequence tool in galaxy. I extracted sequence of this location chr10 123229360 123229525 fgfr2 0 - GAATACTTGGACCTCAGCCAACCTCTCGAACAGTATTCACCTAGTTACCC TGACACAAGAAGTTCTTGTTCTTCAGGAGATGATTCTGTTTTTTCTCCAG ACCCCATGCCTTACGAACCATGCCTTCCTCAGTATCCACACATAAACGGC AGTGTTAAAACATGA And I checked back in UCSC browser by pasting the same location. The sequences are completely different (hg18). Could you please help me in this issue Thanx Gireesh

ADD COMMENT • link written 8.2 years ago by John McPherson • 10

Did you use Galxy FASTA tool ? or UCSC table browser? I used Galaxy I'm sure th sequence Galaxy gave is completely different from UCSC (Only antisense strand). On Fri, Sep 17, 2010 at 7:08 PM, John McPherson

ADD REPLY • link written 8.2 years ago by gireesh bogu • 40

No I extrcated -. But your sense antisense sequences should be the same but in reverse right? But your two sequences are completely different ? Why is that? On Fri, Sep 17, 2010 at 7:08 PM, John McPherson

ADD REPLY • link written 8.2 years ago by gireesh bogu • 40

Hey Gireesh, The sequences are not just reverse but reverse complement, AND they are written ONLY in the 5' to 3' direction. Taking the example of the first 16 bases ( in red) are the reverse complement of the last 16 ( in pink). 5'-3':TTCATGTTTTAACACT 5'-3':AGTGTTAAAACATGAA Now flip the lower sequence around ( write is 3'-5' direction) and the beauty of the DNA strand becomes obvious with A's pairing with T and G with C 5'-3':TTCATGTTTTAACACT 3'-5':AAGTACAAAATTGTGA

ADD REPLY • link written 8.2 years ago by Ruchi Bajpai • 10

Hi evrybody, I would like to align some sequences to maize genome. How I can import it to galaxy?. My sequences are already loaded and I have the "ZmB73_AGPv1_genome.fasta.gz" file (not loaded yet), but I'm not sure if is this that I have to do. Any suggest are wellcome Best regards, Cristian

ADD REPLY • link written 8.2 years ago by Cristian Rojas • 70

Cristian, You can use your FASTA file with the NGS mappers (BWA, Bowtie, Lastz). Galaxy allows you to upload a gzipped file into your history, which it extracts after you upload it. Note that the file should be a single FASTA file containing all chromosomes/scaffolds/etc., each marked with a single header line. (Also, the file can only be gzipped (not tarred and gzipped)--it looks like yours is fine.) Then, when you are going to do the mapping, select the Use one from your history option instead of using one of the built-in indexes. Galaxy will create the indexes that the mapper needs from your supplied FASTA file before it does the mapping. Let us know if you need any further assistance. Regards, Kelly

ADD REPLY • link written 8.2 years ago by Kelly Vincent • 340

Hey Ruchi thanx for detailed explanation :) cheers Gireesh

ADD REPLY • link written 8.2 years ago by gireesh bogu • 40

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