Galaxy

Question: Galaxy

12.8 years ago by

Laura Elnitski • 130 wrote:

Can galaxy put header lines between samples when returning genomic DNA? Other servers want to see the separation of sequences in FASTA files. Thanks, Laura Laura Elnitski, Ph.D. Head Genomic Functional Analysis Section Genome Technology Branch National Human Genome Research Institute National Institutes of Health 5625 Fishers Lane, Rm. 5N-01R Rockville, MD 20852 phone: 301-451-0265 fax: 301-435-6170

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modified 7.8 years ago by Kanwei Li • 270 • written 12.8 years ago by Laura Elnitski • 130

12.8 years ago by

Anton Nekrutenko ♦ 1.7k

Penn State

Anton Nekrutenko ♦ 1.7k wrote:

Fasta headers are lines that start with ">". What exactly do you mean? anton Anton Nekrutenko Assistant Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics 505 Wartik Building PennState University University Park, PA 16802 814 865-4752 814 863-6699 FAX anton@bx.psu.edu http://www.bx.psu.edu/~anton http://g2.bx.psu.edu

ADD COMMENT • link written 12.8 years ago by Anton Nekrutenko ♦ 1.7k

12.8 years ago by

Anton Nekrutenko ♦ 1.7k

Penn State

Anton Nekrutenko ♦ 1.7k wrote:

Do you want to have spaces between FASTA records, so this GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA AGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG looks like this: GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA AGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG Anton Nekrutenko Assistant Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics 505 Wartik Building PennState University University Park, PA 16802 814 865-4752 814 863-6699 FAX anton@bx.psu.edu http://www.bx.psu.edu/~anton http://g2.bx.psu.edu

ADD COMMENT • link written 12.8 years ago by Anton Nekrutenko ♦ 1.7k

12.8 years ago by

Laura Elnitski • 130

Laura Elnitski • 130 wrote:

Hi- I asked for sequence from a list of regions. I got this: GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCAAGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG......continuing for over a hundred thousand bp but I need this format to separate the entries: GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA AGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG etc. thanks, Laura To: Elnitski, Laura (NIH/NHGRI) [E] Cc: galaxy-user@bx.psu.edu Subject: Re: [Galaxy-user] galaxy Do you want to have spaces between FASTA records, so this GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA AGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG looks like this: GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA AGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG Anton Nekrutenko Assistant Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics 505 Wartik Building PennState University University Park, PA 16802 814 865-4752 814 863-6699 FAX anton@bx.psu.edu http://www.bx.psu.edu/~anton http://g2.bx.psu.edu

ADD COMMENT • link written 12.8 years ago by Laura Elnitski • 130

Could you send me your interval file. Thanks, anton Anton Nekrutenko Assistant Professor Department of Biochemistry and Molecular Biology Center for Comparative Genomics and Bioinformatics 505 Wartik Building PennState University University Park, PA 16802 814 865-4752 814 863-6699 FAX anton@bx.psu.edu http://www.bx.psu.edu/~anton http://g2.bx.psu.edu

ADD REPLY • link written 12.8 years ago by Anton Nekrutenko ♦ 1.7k

7.8 years ago by

Kanwei Li • 270

Kanwei Li • 270 wrote:

Hello Musa, I am forwarding this question to the mailing list so that someone better qualified can help you. -K

ADD COMMENT • link written 7.8 years ago by Kanwei Li • 270

Hello Musa, After upload, click on the pencil icon for your dateset and set the metadata so that the file type in the "Change data type" box is "fastq". This will get around any file extension issues. Please let us know if we can help more. As Kanwei stated, data questions are best sent directly to the galaxy-user mailing list. Hopefully this helps! Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

ADD REPLY • link written 7.8 years ago by Jennifer Hillman Jackson ♦ 25k

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