User: tpaisie

gravatar for tpaisie
tpaisie70
Reputation:
70
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Trusted
Location:
University of Florida
Twitter:
tpaisie
Last seen:
4 weeks, 1 day ago
Joined:
3 years, 12 months ago
Email:
t********@gmail.com

Posts by tpaisie

<prev • 44 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 16 months 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 16 months ago by tpaisie70
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Comment: C: Trouble with BLAST using Biopython
... Edited the original question! ...
written 16 months 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 16 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 21 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 21 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 21 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 21 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 2.2 years ago by tpaisie70
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200+ samples to run with SSPACE
... I have around 270 samples of Salmonella. I'm trying to use the program SSPACE to extend and scaffold pre-assembled contigs. Here is my set up of the library.txt file (with less samples): SRR1122483 bowtie SRR1122483_pair_1.fastq SRR1122483_pair_2.fastq 200 0.75 FR SRR1122484 bowtie SRR112 ...
assembly next-gen snp written 2.2 years ago by tpaisie70

Latest awards to tpaisie

Popular Question 4 weeks ago, created a question with more than 1,000 views. For Running iqtree in a python script?
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Running Freebayes on 100+ Samples
Great Question 4 months ago, created a question with more than 5,000 views. For Help with ggtree tip labeling in R
Popular Question 7 months ago, created a question with more than 1,000 views. For Minimum spanning tree - coloring the nodes
Popular Question 12 months ago, created a question with more than 1,000 views. For Minimum spanning tree - coloring the nodes
Popular Question 12 months ago, created a question with more than 1,000 views. For Help with ggtree tip labeling in R
Scholar 16 months ago, created an answer that has been accepted. For A: Trouble with BLAST using Biopython
Popular Question 20 months ago, created a question with more than 1,000 views. For Changing names of Fasta headers
Popular Question 23 months ago, created a question with more than 1,000 views. For Help with ggtree tip labeling in R
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Help with ggtree tip labeling in R
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Extracting Gene nucleotide sequences from a Genbank files using Biopython
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Help with ggtree tip labeling in R
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Filtering sequences from a Fasta file using Biopython

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