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 John.McPherson@oicr.on.cawrote:

I think that you have extracted the “+” strand for your comparison. Below is the “-” strand from UCSC hg18

...

hg18_dna range=chr10:123229360-123229525 5'pad=0 3'pad=0 strand=+

repeatMasking=lower TTCATGTTTTAACACTGCCGTTTATGTGTGGATACTGAGGAAGGCATGGT TCGTAAGGCATGGGGTCTGGAGAAAAAACAGAATCATCTCCTGAAGAACA AGAACTTCTTGTGTCAGGGTAACTAGGTGAATACTGTTCGAGAGGTTGGC TGAGGTCCAAGTATTC

...

hg18_dna range=chr10:123229360-123229525 5'pad=0 3'pad=0 strand=-

repeatMasking=lower GAATACTTGGACCTCAGCCAACCTCTCGAACAGTATTCACCTAGTTACCC TGACACAAGAAGTTCTTGTTCTTCAGGAGATGATTCTGTTTTTTCTCCAG ACCCCATGCCTTACGAACCATGCCTTCCTCAGTATCCACACATAAACGGC

AGTGTTAAAACATGAA

On 10-09-16 11:28 PM, "gireesh bogu" gireeshkbogu@gmail.com wrote:

Dear Galaxy

I found a bug in extracting FATSA sequence tool in galaxy.

I extracted sequence of this location chr10 123229360 123229525 fgfr2 0 -

...

hg18_chr10_123229360_123229525_-

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

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

On Fri, Sep 17, 2010 at 7:08 PM, John McPherson John.McPherson@oicr.on.ca wrote: I think that you have extracted the “+” strand for your comparison. Below is the “-” strand from UCSC hg18

...

hg18_dna range=chr10:123229360-123229525 5'pad=0 3'pad=0 strand=+ repeatMasking=lower

TTCATGTTTTAACACTGCCGTTTATGTGTGGATACTGAGGAAGGCATGGT TCGTAAGGCATGGGGTCTGGAGAAAAAACAGAATCATCTCCTGAAGAACA AGAACTTCTTGTGTCAGGGTAACTAGGTGAATACTGTTCGAGAGGTTGGC TGAGGTCCAAGTATTC

...

hg18_dna range=chr10:123229360-123229525 5'pad=0 3'pad=0 strand=- repeatMasking=lower

GAATACTTGGACCTCAGCCAACCTCTCGAACAGTATTCACCTAGTTACCC TGACACAAGAAGTTCTTGTTCTTCAGGAGATGATTCTGTTTTTTCTCCAG ACCCCATGCCTTACGAACCATGCCTTCCTCAGTATCCACACATAAACGGC AGTGTTAAAACATGAA

On Sep 17, 2010, at 5:52 PM, gireesh bogu wrote:

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 John.McPherson@oicr.on.ca wrote: I think that you have extracted the “+” strand for your comparison. Below is the “-” strand from UCSC hg18

...

hg18_dna range=chr10:123229360-123229525 5'pad=0 3'pad=0 strand=+ repeatMasking=lower

TTCATGTTTTAACACTGCCGTTTATGTGTGGATACTGAGGAAGGCATGGT TCGTAAGGCATGGGGTCTGGAGAAAAAACAGAATCATCTCCTGAAGAACA AGAACTTCTTGTGTCAGGGTAACTAGGTGAATACTGTTCGAGAGGTTGGC TGAGGTCCAAGTATTC

...

hg18_dna range=chr10:123229360-123229525 5'pad=0 3'pad=0 strand=- repeatMasking=lower

GAATACTTGGACCTCAGCCAACCTCTCGAACAGTATTCACCTAGTTACCC TGACACAAGAAGTTCTTGTTCTTCAGGAGATGATTCTGTTTTTTCTCCAG ACCCCATGCCTTACGAACCATGCCTTCCTCAGTATCCACACATAAACGGC AGTGTTAAAACATGAA

On 10-09-16 11:28 PM, "gireesh bogu" gireeshkbogu@gmail.com wrote:

Dear Galaxy

I found a bug in extracting FATSA sequence tool in galaxy.

I extracted sequence of this location chr10 123229360 123229525 fgfr2 0 -

...

hg18_chr10_123229360_123229525_-

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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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

On Sep 18, 2010, at 3:43 PM, Cristian Rojas wrote:

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

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