User: tpaisie

gravatar for tpaisie
tpaisie70
Reputation:
70
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Trusted
Location:
University of Florida
Twitter:
tpaisie
Last seen:
2 days, 21 hours ago
Joined:
2 years, 10 months ago
Email:
t********@gmail.com

Posts by tpaisie

<prev • 45 results • page 1 of 5 • next >
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Answer: A: Trouble with BLAST using Biopython
... I got the script to work finally! Some set up must have been off on my computer or with my biopython! ...
written 8 weeks ago by tpaisie70
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Comment: C: Trouble with BLAST using Biopython
... I added this to my code and only got this in terminal: ValueError: I/O operation on closed file ...
written 8 weeks ago by tpaisie70
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Comment: C: Trouble with BLAST using Biopython
... Edited the original question! ...
written 8 weeks ago by tpaisie70
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Trouble with BLAST using Biopython
... I have been using Biopython to make scripts to run sequences through BLAST. I'm using the command: NCBIWWW.qblast() Here is the beginning of most of my scripts: import sys, os from Bio import SeqIO, Entrez, SearchIO from Bio.Blast import NCBIWWW, NCBIXML from ftplib import ...
ncbi python blast written 8 weeks ago by tpaisie70
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Comment: C: Running Freebayes on 100+ Samples
... That worked!!! Thank you so much for your help!! ...
written 7 months ago by tpaisie70
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Comment: C: Running Freebayes on 100+ Samples
... So I did some looking at my bam file headers and noticed that some of the samples were ran with different versions of bowtie2. Do you think that could potentially be the issue? ...
written 7 months ago by tpaisie70
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Comment: C: Running Freebayes on 100+ Samples
... Those samples were part of the list, but it seems like it never even gets past the first sample. I took out the sample I mentioned in the error out of the list to see if it was just sample, and it just gave the same error with the next sample. So I have no idea what is going on. ...
written 7 months ago by tpaisie70
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Comment: C: Running Freebayes on 100+ Samples
... Yeah I have, it's still not running. I've checked that many times, because originally I did think that was the problem. ...
written 7 months ago by tpaisie70
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Running Freebayes on 100+ Samples
... Hi everyone, So I've been using Freebayes for a while now to do my variant calling with usually around 100-200 samples and I've never had a problem running it before. I usually make a text file with my list of bam files (everything is in the same directory and my bam files are indexed). I've ac ...
variant calling bacteria snp written 7 months ago by tpaisie70
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Comment: C: 200+ samples to run with SSPACE
... So I have my library.txt file already made with all the samples I want to run included in it, but I am unable to run all these samples at the same time or even sequentially. I have been having to do run this program one sample at a time. For example, I have to change my library.txt file to: S ...
written 12 months ago by tpaisie70

Latest awards to tpaisie

Scholar 8 weeks ago, created an answer that has been accepted. For A: Trouble with BLAST using Biopython
Popular Question 6 months ago, created a question with more than 1,000 views. For Changing names of Fasta headers
Popular Question 9 months ago, created a question with more than 1,000 views. For Help with ggtree tip labeling in R
Popular Question 14 months ago, created a question with more than 1,000 views. For Help with ggtree tip labeling in R
Popular Question 15 months ago, created a question with more than 1,000 views. For Extracting Gene nucleotide sequences from a Genbank files using Biopython
Popular Question 18 months ago, created a question with more than 1,000 views. For Help with ggtree tip labeling in R
Popular Question 19 months ago, created a question with more than 1,000 views. For Filtering sequences from a Fasta file using Biopython

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