User: dally

gravatar for dally
dally160
Reputation:
160
Status:
Trusted
Location:
United States
Last seen:
1 year, 4 months ago
Joined:
2 years, 8 months ago
Email:
c******************@gmail.com

Posts by dally

<prev • 80 results • page 1 of 8 • next >
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Comment: C: a problem with peak annotation after ChIP-seq
... It must be removed, HOMER is peculiar about this. ...
written 20 months ago by dally160
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Comment: C: How to get native bash in Windows 10
... My question is, how do you find the path where your bash stores files? Does everything have to be moved using the command line or can you use the File Explorer to move files in and out? ...
written 22 months ago by dally160
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Comment: C: SRAtoolkit error during fastq-dump
... This actually ended up being the answer. Just had to add my proxy settings to the configuration file. Thanks a ton piet. ...
written 2.4 years ago by dally160
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Comment: C: SRAtoolkit error during fastq-dump
... They sadly do not appear to have any fastq files for download. ...
written 2.4 years ago by dally160
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Comment: C: SRAtoolkit error during fastq-dump
... Sorry, EBI was incorrect, I got the SRA files from GEO. ...
written 2.4 years ago by dally160
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SRAtoolkit error during fastq-dump
... I downloaded an SRA file from GEO FTP. I then ran the following command trying to grab the fastq files, but I keep coming up with this error and I can't find anything about it on google. Here's the command used: fastq-dump --split-3 '/path/to/SRR1460694.sra' Error: fastq-dump.2.5.7 err: connec ...
software error sratoolkit fastq-dump chip-seq written 2.4 years ago by dally160 • updated 2.4 years ago by piet1.4k
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Comment: C: Discovering motifs for core promoter elements on a set of enhancer sites
... Would you know a database that contains mammalian promoter sequences that have an annotated TATA box? Some of the papers I read mentioned obtaining a list from GenBank, but i'm not having much luck. I want to validate some of the motifs I have found. ...
written 2.4 years ago by dally160
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Comment: C: Discovering motifs for core promoter elements on a set of enhancer sites
... It's amazing that none of these have the actual promoter element motifs i'm looking for (at least not the free version of TRANSFAC). I have found a few drosophila motifs, but working with human data I don't really know how reliable this would be. ...
written 2.4 years ago by dally160
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Comment: C: Discovering motifs for core promoter elements on a set of enhancer sites
... I'll give FIMO a try. I seem to have been having a hard time finding PWM's for my targets of interest (finding only TBP and Sp1) in homo sapiens. I find it hard to believe there is not already motifs for the other guys, but JASPAR seems to not have them, and my search is bringing up nothing.  Will ...
written 2.4 years ago by dally160
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Comment: C: Discovering motifs for core promoter elements on a set of enhancer sites
... If anything this gives me excellent information to go on. I will probably use centrimo and then compare it to the results from AME/FIMO, which does not focus on motif position. ...
written 2.4 years ago by dally160

Latest awards to dally

Popular Question 18 months ago, created a question with more than 1,000 views. For Pearson Correlation test between two Chip-Seq data sets
Popular Question 20 months ago, created a question with more than 1,000 views. For Pearson Correlation test between two Chip-Seq data sets
Popular Question 20 months ago, created a question with more than 1,000 views. For Pearson Correlation test between two Chip-Seq data sets
Student 2.3 years ago, asked a question with at least 3 up-votes. For Generating Gencode TSS file
Supporter 2.4 years ago, voted at least 25 times.
Rising Star 2.5 years ago, created 50 posts within first three months of joining.

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