User: Sequencegeek

gravatar for Sequencegeek
Sequencegeek730
Reputation:
730
Status:
New User
Location:
UCLA
Last seen:
5 years, 10 months ago
Joined:
6 years, 9 months ago
Email:
c***********@gmail.com

I do post transcriptional research at UCLA.

Posts by Sequencegeek

<prev • 38 results • page 1 of 4 • next >
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Blast W/ G:T Pairing?
... I'm using BLAST for a part of my pipeline and need to change my pipeline to allow G/U matching. My google foo isn't getting me very far. Does anyone know if there is a similar version of BLAST with this capability? Thanks ...
mapping blast written 5.9 years ago by Sequencegeek730 • updated 5.9 years ago by Larry_Parnell16k
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Comment: C: Irc Channel Or Popular Real-Time Bio Hangouts
... Yeah but it's not as involved and not real-time. The cool part about IRC is you start to have a sense of community by chatting with people that are in your same field and you can have an involved discussion with them - even if it's the same 3 people. If they are doing bioinformatics then they like ...
written 6.2 years ago by Sequencegeek730
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Comment: C: Irc Channel Or Popular Real-Time Bio Hangouts
... haha, so nineties? Twitter is so for my little sister ;) (it has it's uses, though) ...
written 6.2 years ago by Sequencegeek730
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Comment: C: Irc Channel Or Popular Real-Time Bio Hangouts
... Maybe we should make a #biostar IRC? I've never made one before but It shouldn't be too hard....right? ...
written 6.2 years ago by Sequencegeek730
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Irc Channel Or Popular Real-Time Bio Hangouts
... Hi everyone, So biostar is obviously a great place to discuss answers to typical questions we all have. Usually I read the questions and answers just to see if there are ways of doing things or using tools I haven't thought/heard of. That being said, does anyone know of any IRC channels to share ...
written 6.2 years ago by Sequencegeek730 • updated 3.8 years ago by Biostar ♦♦ 20
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Answer: A: Guessing The Quality Scale In Fastq Files
... In addition to Ryan, I have a python based fastq quality guesser as well if you would like to use it. It is just standard python (no biopython). PM if interested. ...
written 6.3 years ago by Sequencegeek730
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Answer: A: How To Efficiently Parse A Huge Fastq File?
... You could also use a binary search. I have a library in Python that will only require you to write a small function to adapt to your file type... ...
written 6.3 years ago by Sequencegeek730
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Answer: A: How To Organize A Pipeline Of Small Scripts Together?
... Something I've found useful in python is to set up a framework that allows me to run specific functions in a module from the command line. This allows all the similar scripts (usually data aggregation, plotting, and analysis) to be put into a single module and each step ran from the command line. ...
written 6.4 years ago by Sequencegeek730
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Answer: A: Dna Secondary Structure Prediction Of A Large Dataset
... Hi There, If you are interested in more detailed information about the hairpin, there is a script on this page that will parse the RNAFold output. It may be a little buggy but it has worked for me in the past. RNA fold Topic ...
written 6.4 years ago by Sequencegeek730
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Comment: C: What Are The Most Common Stupid Mistakes In Bioinformatics?
... I have an opposite mistake. I accidentally replace a string in the whole document and something I didn't want to replace gets replaced. Now I visually select the area where I want to replace... ...
written 6.4 years ago by Sequencegeek730

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