User: julestrachsel

gravatar for julestrachsel
Reputation:
20
Status:
New User
Location:
United States
Last seen:
1 year, 6 months ago
Joined:
2 years, 11 months ago
Email:
j************@gmail.com

Posts by julestrachsel

<prev • 7 results • page 1 of 1 • next >
1
vote
0
answers
669
views
0
answers
biopython script using MUSCLE stalls with >300 sequences
... Hello, I am trying to learn biopython a little better and I am tyring to write a python script that will take in some unaligned DNA sequences in fasta format from the command line, translate these to protein sequences, align these sequences with MUSCLE, and then write out the resulting protein alig ...
sequence alignment biopython written 20 months ago by julestrachsel20
0
votes
11
answers
29k
views
11
answers
Comment: C: Selecting Random Pairs From Fastq?
... I am having an issue using seqtk to subsample some illumina reads prior to assembly with MIRA.  I got the following message after I tried to subsample 1,000,000 reads from an illumina fastq paired end file: "MIRA found duplicate read names in your data (see log above for more info).  * *            ...
written 2.3 years ago by julestrachsel20
1
vote
1
answer
1.2k
views
1
answers
Comment: C: Deconseq database generation issues
... Thank you! I really should have learned more about bwa first.  I used "-a is" in my database generation command on the mitochondrial genome and it worked like a dream.   Thanks again!!   ...
written 2.3 years ago by julestrachsel20
5
votes
1
answer
1.2k
views
1
answer
Deconseq database generation issues
... Hello!   I am attempting to remove host cell line reads from viral reads for a viral genome sequencing effort.  (Miseq 2x300 Nextera).  I downloaded and set up deconseq according to the install file, and generated a database using bwa64 on my desired genome.  This worked great and I was able to fi ...
genome assembly deconseq bwa sequencing written 2.3 years ago by julestrachsel20 • updated 2.3 years ago by 5heikki6.6k
1
vote
2
answers
1.7k
views
2
answers
Answer: A: How to output a new alignment containing only sequences with a particular residu
... Thank you so much for the answer! It was just the advice I needed. This is the python file I made to accomplish my goal (it's probably really ugly to anyone who has actual python experience) from Bio import AlignIO from Bio.Align import MultipleSeqAlignment alignment = AlignIO.read("MyProt.fasta ...
written 2.9 years ago by julestrachsel20
0
votes
2
answers
1.7k
views
2
answers
Comment: C: How to output a new alignment containing only sequences with a particular residu
... Thank you so much for the answer! It was just the advice I needed. This is the python file I made to accomplish my goal (it's probably really ugly to anyone who has actual python experience) from Bio import AlignIO from Bio.Align import MultipleSeqAlignment alignment = AlignIO.read("MyProt.fasta ...
written 2.9 years ago by julestrachsel20
7
votes
2
answers
1.7k
views
2
answers
How to output a new alignment containing only sequences with a particular residue in a specified column
... Hello! I am very new to biopython and I am trying to accomplish what I think is a simple task:  I would like to remove sequences from a protein alignment that do not contain a particular residue at a specified position.  I would like to be able to input a protein alignment in fasta format and then ...
alignment biopython written 2.9 years ago by julestrachsel20

Latest awards to julestrachsel


Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1477 users visited in the last hour