GENE AND CHROMOSOME SEARCHES

Question: GENE AND CHROMOSOME SEARCHES

2.2 years ago by

irusk • 10

Canada

irusk • 10 wrote:

HI I WAS WONDERING ONCE YOU LOAD UP A VCF FILE HOW DO YOU LOOK AT SPECIFIC AREAS AND CHROMOSOMES INSTEAD OF STARTING FROM CHR 1 AND GOING THROUGH ALL THE CHROMOSOMES TO FIND THE ONE YOU WANT? SORRY FOR THE QUESTION BUT I AM JUST NEW AT THIS!

THANK YOU INGRID

snp • 649 views

ADD COMMENT • link •

modified 2.2 years ago by Martin Čech ♦♦ 4.9k • written 2.2 years ago by irusk • 10

Hello, Please avoid using all caps next post. Thanks! Jen, Galaxy team

ADD REPLY • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

2.2 years ago by

Devon Ryan • 1.9k

Germany

Devon Ryan • 1.9k wrote:

Load it in IGV
If you instead want the raw text, use "bedtools intersect".

ADD COMMENT • link written 2.2 years ago by Devon Ryan • 1.9k

2.2 years ago by

irusk • 10

Canada

irusk • 10 wrote:

THANKS DEVON , I WILL TRY IT :)

ADD COMMENT • link written 2.2 years ago by irusk • 10

2.2 years ago by

irusk • 10

Canada

irusk • 10 wrote:

Hi , I entered my bam file into "bed tools intersect" which it loaded up fine but would not let me look up info. It said " The uploaded binary file contains inappropriate content"???? Have you ever seen that? Maybe I loaded it wrong or maybe the lab doesn't want me to see something. Any help would be helpful.

ADD COMMENT • link written 2.2 years ago by irusk • 10

VCF files shouldn't be binary, so I haven't a clue why that's happening.

ADD REPLY • link written 2.2 years ago by Devon Ryan • 1.9k

This is a protection machanism of Galaxy. All binary files are scanned for certain binary tags to figure out what the actual file format is. If none of those tags can be found Galaxy will give this warning. This means your uploaded file is neither a valid BAM file nor a VCF file, but is a binary file of a format that Galaxy does not understand.

ADD REPLY • link written 2.2 years ago by y.hoogstrate • 460

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