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
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 On Mar 2, 2006, at 10:43 PM, Laura Elnitski 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
_______________________________________________ Galaxy-user mailing list Galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Do you want to have spaces between FASTA records, so this
hg17_chr1_148022106_148022312_+ GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA hg17_chr1_148052068_148052136_+ AGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG
looks like this:
hg17_chr1_148022106_148022312_+ GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA
hg17_chr1_148052068_148052136_+ 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 On Mar 2, 2006, at 10:43 PM, Laura Elnitski 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
_______________________________________________ Galaxy-user mailing list Galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
Hi- I asked for sequence from a list of regions. I got this:
hg17_chr1_148022106_148022312_+ GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCAAGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG......continuing for over a hundred thousand bp
but I need this format to separate the entries:
hg17_chr1_148022106_148022312_+ GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA hg17_chr1_148052068_148052136_+ AGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG
next one etc.
thanks, Laura -----Original Message----- From: Anton Nekrutenko [mailto:anton@bx.psu.edu] Sent: Fri 3/3/2006 8:54 AM 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
hg17_chr1_148022106_148022312_+ GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA hg17_chr1_148052068_148052136_+ AGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG
looks like this:
hg17_chr1_148022106_148022312_+ GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA
hg17_chr1_148052068_148052136_+ 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 On Mar 2, 2006, at 10:43 PM, Laura Elnitski 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
_______________________________________________ Galaxy-user mailing list Galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
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 On Mar 3, 2006, at 9:04 AM, Elnitski, Laura ((NIH/NHGRI)) [E] wrote:
Hi-
I asked for sequence from a list of regions. I got this:
hg17_chr1_148022106_148022312_+ GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCAAGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG......continuing for over a hundred thousand bp
but I need this format to separate the entries:
hg17_chr1_148022106_148022312_+ GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA hg17_chr1_148052068_148052136_+ AGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG
next one etc.
thanks, Laura
-----Original Message----- From: Anton Nekrutenko [mailto:anton@bx.psu.edu] Sent: Fri 3/3/2006 8:54 AM 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
hg17_chr1_148022106_148022312_+ GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA hg17_chr1_148052068_148052136_+ AGTTTGGCCAGGCGGAATCAGCAGACATTGATGCCAGCTCAGCTATGGAC ACATCTGAGCCAGCCAAG
looks like this:
hg17_chr1_148022106_148022312_+ GTGCTGCAGAGCTTCAAGATAATGGATTACAGCCTCTTGATGTCAATCCA TAATATAGATCATGCACAACGAGAGCCCTTAAGCAGTGAAACACAGTACT CAGTTGATACTCGAAGACCGGCCCCCCAAAAGGCTCTGTATTCCACAGCC ATGGAATCCATCCAGGGAGAGGCTCGACGGGGTGGTACCATGGAGACTGA TGACCA
hg17_chr1_148052068_148052136_+ 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
On Mar 2, 2006, at 10:43 PM, Laura Elnitski 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
_______________________________________________ Galaxy-user mailing list Galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user
participants (3)
-
Anton Nekrutenko -
Elnitski, Laura (NIH/NHGRI) [E] -
Laura Elnitski