User: mshumph2

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mshumph20
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Posts by mshumph2

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Comment: C: Bedtools getfasta outputting a blank file
... Thanks for the help! I downloaded pyfaidx and now I'm getting text, but only one line. So it looks something like: >chr1 AATCCCCAAAAGTTT And then it stops after that first line. Any suggestions? ...
written 4.7 years ago by mshumph20
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Comment: C: Bedtools getfasta outputting a blank file
... I'm not sure what a head is, but this is the format it's in. As you can see the format changes a few coordinates down. Also, copying and pasting changes the spacing between the columns.   chr1    9885764    9885814    chr1:9885764-9885814 chr1    9903769    9903819    chr1:9903769-9903819 chr1     ...
written 4.7 years ago by mshumph20
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Bedtools getfasta outputting a blank file
... Hi, I'm using bedtools getfasta to get a bunch of sequences from chromosome 1. I have "chr1.fa" (from UCSC Genome Browser) as the input fasta file, and I have a BED file with chromosome location, start, stop, and name columns. My input looks like this: bedtools getfasta -fi chr1.fa -bed bedfile.bed ...
sequence written 4.7 years ago by mshumph20 • updated 4.7 years ago by Matt Shirley9.0k
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Querying the UCSC Genome Browser for DNA sequences (large collection of data)
... I have a spreadsheet with 500 different positions on different chromosomes, and I'd like to pull out the DNA sequences between those positions. The spreadsheet is already set up in a way that could easily be related to the UCSC Genome Browser database if only I had a way to either upload my spreadsh ...
sequence written 4.7 years ago by mshumph20 • updated 4.7 years ago by mickael.leclercq30

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