User: tpaisie

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tpaisie70
Reputation:
70
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Trusted
Location:
University of Florida
Twitter:
tpaisie
Last seen:
11 hours ago
Joined:
2 years, 4 months ago
Email:
t********@gmail.com

Posts by tpaisie

<prev • 41 results • page 1 of 5 • next >
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Comment: C: Running Freebayes on 100+ Samples
... That worked!!! Thank you so much for your help!! ...
written 27 days 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 28 days 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 28 days 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 28 days 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 28 days 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 6 months 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 6 months ago by tpaisie70
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Comment: C: Changing names of Fasta headers
... Ohh thank you so much that worked!!!! ...
written 9 months ago by tpaisie70
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Comment: C: Changing names of Fasta headers
... So yes your interpretation of what I would like is correct. Although I used your command and I'm getting this as an error: sed: 1: "HC1993.fa": extra characters at the end of H command And it is not making the new fasta files with the new headers. ...
written 9 months ago by tpaisie70
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Changing names of Fasta headers
... So I have a director full of fasta files and I want to change the fasta header in each one by the name of their corresponding fasta file. For example: HC1993.fa > X58834 CCTGCATCTGCAA HC1993.fa > HC1993 CCTGCATCTGCAA I have about 50 fasta files like that in a directory th ...
fasta sequence sed unix bash loop written 9 months ago by tpaisie70 • updated 6 months ago by h.mon22k

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Popular Question 14 days ago, created a question with more than 1,000 views. For Changing names of Fasta headers
Popular Question 3 months ago, created a question with more than 1,000 views. For Help with ggtree tip labeling in R
Popular Question 8 months ago, created a question with more than 1,000 views. For Help with ggtree tip labeling in R
Popular Question 9 months ago, created a question with more than 1,000 views. For Extracting Gene nucleotide sequences from a Genbank files using Biopython
Popular Question 12 months ago, created a question with more than 1,000 views. For Help with ggtree tip labeling in R
Popular Question 13 months ago, created a question with more than 1,000 views. For Filtering sequences from a Fasta file using Biopython

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