User: SaltedPork

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SaltedPork80
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Posts by SaltedPork

<prev • 49 results • page 1 of 5 • next >
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Answer: A: How do you use BLAST?
... I use Blast mainly to aid in typing viral sequences. This info is then copied into a spreadsheet, and there is no filtering involved usually. ...
written 10 months ago by SaltedPork80
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Comment: C: How to get list of different bases and their positions from an alignment?
... they are about 92% similar, ~700 base difference ...
written 10 months ago by SaltedPork80
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Comment: C: How to get list of different bases and their positions from an alignment?
... Hi, just the sequences i'm comparing. ...
written 10 months ago by SaltedPork80
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How to get list of different bases and their positions from an alignment?
... I am aligning two viral genomes which I am expecting to be >90% similar. I would like a list of the changes (from one base to another) and their locations in the genome. Which program(s) can I use to achieve this? I have already tried lastz's --census option, but it only tells you if a base is al ...
alignment written 10 months ago by SaltedPork80 • updated 10 months ago by WouterDeCoster37k
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In Jalview, how can I colour just the nucleotides that are different between sequences
... I have 3 sequences in Jalview, they are around 90% identity when doing a single alignment against each other, how can I show with colour which bases differ? The nucleotide options colours all bases... ...
alignment jalview written 10 months ago by SaltedPork80
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Answer: A: Interesting/useful/beautiful bio sequence viz tools
... Circos and IGV I would recommend ...
written 12 months ago by SaltedPork80
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Comment: C: Getting a bash pipeline to output non-zero exit code when a step fails
... Thanks, this is a really good solution. Do you have any advice for if I wanted to just have the pipeline fail at certain points in the pipeline. Perhaps put a command in a loop and check that echo $? returns non-zero or not? ...
written 12 months ago by SaltedPork80
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Getting a bash pipeline to output non-zero exit code when a step fails
... I have a pipeline which looks something like below, its written in bash Trimmomatic --> Samtools --> Smalt --> Lastz --> custom perl programs. If anyone of those processes fails they usually return a non-0 exit code, usually a `1`. However, my pipeline program will continue to run, rep ...
bash sh command-line written 12 months ago by SaltedPork80 • updated 12 months ago by bernatgel1.8k
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Comment: C: How to convert string into fasta using bash?
... Pierre mate, I feel pretty silly given how simple the solution is. Thanks! ...
written 13 months ago by SaltedPork80
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How to convert string into fasta using bash?
... Hi, I have a string of a fasta file (see below). You can see it's already in a fasta format, but its got spaces in the ID, and has newline characters. I have a Perl solution for this, but it's a bit hokey. I was wondering if any of you have the bash skills to turn this into a regular fasta? Input: ...
fasta perl string bash written 13 months ago by SaltedPork80 • updated 13 months ago by Pierre Lindenbaum118k

Latest awards to SaltedPork

Popular Question 15 days ago, created a question with more than 1,000 views. For How can I use Samtools to map coverage distribution?
Popular Question 7 months ago, created a question with more than 1,000 views. For How can I use Samtools to map coverage distribution?
Popular Question 7 months ago, created a question with more than 1,000 views. For Getting a bash pipeline to output non-zero exit code when a step fails
Popular Question 8 months ago, created a question with more than 1,000 views. For Using BWA Index and i get 5 output files, but BWA-mem asks for just 1
Voter 11 months ago, voted more than 100 times.
Supporter 15 months ago, voted at least 25 times.
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Using BWA Index and i get 5 output files, but BWA-mem asks for just 1

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