A Question Regarding Sequence Retrieval

Question: A Question Regarding Sequence Retrieval

8.7 years ago by

pande • 110

pande • 110 wrote:

Dear Galaxy, I have the results for the sequence retrieval for Insulator regions in the human genome and I am having difficulty in comprehending the upper and lower case associated with my sequences.I know it for sure that they are regions which do not in any way overlap with exons or introns and are that between any 2 genes. I am attaching a small part of the sequence file for you to see and help me. warm regards, Amit.

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modified 8.7 years ago by Guruprasad Ananda • 230 • written 8.7 years ago by pande • 110

8.7 years ago by

Guruprasad Ananda • 230

Guruprasad Ananda • 230 wrote:

Hello Amit, The genomic sequences hosted on Galaxy are from UCSC and according to their convention repeats from RepeatMasker and Tandem Repeats Finder (with a period of 12 or less) are shown in lower case and non- repeating sequence is shown in upper case. Hope this answers your question. Thanks for using Galaxy, Guru. Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University

ADD COMMENT • link written 8.7 years ago by Guruprasad Ananda • 230

8.7 years ago by

Guruprasad Ananda • 230

Guruprasad Ananda • 230 wrote:

Hi, Using the interval file which you used to fetch fasta sequences, you'll be able to fetch human-chimp alignments. Please use "Extract pairwise MAF blocks" tool under "Fetch alignments" and select "hg18,panTro2" as MAF source. If the MAF source field is empty, please make sure that the database build of your input interval file is set to 'hg18'. Please feel free to email us if you have any further questions. Thanks, Guru. Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University

ADD COMMENT • link written 8.7 years ago by Guruprasad Ananda • 230

8.7 years ago by

Guruprasad Ananda • 230

Guruprasad Ananda • 230 wrote:

Hi Amit, I was not able to reproduce the issue reported by you. I downloaded the BED file from the website pointed by you, and fetched sequences successfully. I'm sharing my history with you: http://main.g2.bx.psu.edu/u/guru/h/test-for-amit Please make sure that you have the correct BED file, and correct metadata settings (chr,start,end columns and genome build). Also, in future, can you please report your questions/issues to one of our mailing lists: galaxy-user@bx.psu.edu, galaxy-bugs@bx.psu.edu? Thanks, Guru. Guruprasad Ananda Graduate Student Bioinformatics and Genomics The Pennsylvania State University

ADD COMMENT • link written 8.7 years ago by Guruprasad Ananda • 230

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