User: Chris Warth

gravatar for Chris Warth
Chris Warth90
Reputation:
90
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Trusted
Location:
United States
Last seen:
1 year, 8 months ago
Joined:
6 years, 10 months ago
Email:
c******@gmail.com

Posts by Chris Warth

<prev • 10 results • page 1 of 1 • next >
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Comment: C: How To Remove The Same Sequences In The Fasta Files?
... yifangt, one of us is certainly confused.   None of your input sequences are duplicated.  Feed seqmagick a file with some duplicated sequences and it will work. ...
written 21 months ago by Chris Warth90
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Comment: C: How To Remove The Same Sequences In The Fasta Files?
... I think this is the only answer that actually works if your fasta file contains a multiple sequence alignment. Both fastx_collapser and gt sequniq fail because they consider '–' to be an invalid character in a fasta sequence.  I didn't ask those tools to validate the sequences, and that's not their ...
written 23 months ago by Chris Warth90
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Comment: C: R: Parsing Fasta From Strings In R?
... Thank you for an equally good solution. The textConnection(COI) solution is pretty much what I expected the solution to look like. ...
written 4.1 years ago by Chris Warth90
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Comment: C: R: Parsing Fasta From Strings In R?
... Thanks for the extensive reply. It looks like this has annoyed you as well. I thought I must be missing something simple but it sounds like it's just an annoying interface. It's too bad because SeqIO makes this very easy in python. ...
written 4.1 years ago by Chris Warth90
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R: Parsing Fasta From Strings In R?
... My goal is to retrieve DNA gene sequence from NCBI using R, but I get stuck trying to parse FASTA sequences from strings. I can get a FASTA string for a gene by using efetch from the Bioconductor genomes package. handle = efetch("NM_009790", db="nucleotide", rettype="fasta") This returns a s ...
fasta R ncbi written 4.1 years ago by Chris Warth90 • updated 4.1 years ago by Neilfws47k
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Comment: C: Counting Short-Read Gene Alignments With Bowtie/Tophat.
... Thanks for the pointer. I thought I was going to have to code my own overlap-finder in python so rolling my own script to work with HTSeq shouldn't be a problem. ...
written 6.8 years ago by Chris Warth90
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Comment: C: Counting Short-Read Gene Alignments With Bowtie/Tophat.
... Being a novice, I'm not sure I understand the question. Tophat outputs a "junctions.bed" file with splice sites that it has discovered without reference to a pre-existing gene map (although you can provide a file of known genes to help it avoid spurious junctions.) ...
written 6.8 years ago by Chris Warth90
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Comment: C: Counting Short-Read Gene Alignments With Bowtie/Tophat.
... Thank you very much. I'll look into using BEDTools as an overlap finder. ...
written 6.8 years ago by Chris Warth90
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Comment: C: Counting Short-Read Gene Alignments With Bowtie/Tophat.
... Thanks you very much. I'll look into using BEDTools as an overlap finder. ...
written 6.8 years ago by Chris Warth90
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7 follow
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Counting Short-Read Gene Alignments With Bowtie/Tophat.
... Let me start by saying I am very new to this so I may be asking naive questions. I am aligning short-reads against the mm9 mouse genome using tophat (which uses bowtie, of course). What I would like to get is a count of how many times each known gene is hit by one of the reads. I have seen sug ...
gene tophat alignment written 6.8 years ago by Chris Warth90 • updated 6.8 years ago by Ryan Dale4.5k

Latest awards to Chris Warth

Popular Question 4.1 years ago, created a question with more than 1,000 views. For Counting Short-Read Gene Alignments With Bowtie/Tophat.
Appreciated 6.8 years ago, created a post with more than 5 votes. For Counting Short-Read Gene Alignments With Bowtie/Tophat.
Good Question 6.8 years ago, asked a question that was upvoted at least 5 times. For Counting Short-Read Gene Alignments With Bowtie/Tophat.
Popular Question 6.8 years ago, created a question with more than 1,000 views. For Counting Short-Read Gene Alignments With Bowtie/Tophat.
Student 6.8 years ago, asked a question with at least 3 up-votes. For Counting Short-Read Gene Alignments With Bowtie/Tophat.

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