User: SaltedPork

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SaltedPork70
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Posts by SaltedPork

<prev • 44 results • page 1 of 5 • next >
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Answer: A: Interesting/useful/beautiful bio sequence viz tools
... Circos and IGV I would recommend ...
written 4 weeks ago by SaltedPork70
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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 7 weeks ago by SaltedPork70
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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 7 weeks ago by SaltedPork70 • updated 7 weeks ago by bernatgel1.0k
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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 9 weeks ago by SaltedPork70
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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 9 weeks ago by SaltedPork70 • updated 9 weeks ago by Pierre Lindenbaum106k
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Comment: C: Any ideas on converting IUPAC ambiguity codes in a fasta file
... Yep, that would be the idea, I suppose I could take this and have many if statements, but then how do I account for sequences which have multiple IUPAC codes in them? ...
written 9 weeks ago by SaltedPork70
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Any ideas on converting IUPAC ambiguity codes in a fasta file
... Hi, I have fasta files that contain ambiguity codes. And I would like to convert the sequences so that it's just ACGT and create a new entry for each possibility. i.e. Y = C or T >sampleID AGCTAGYACG into >sampleID.1 AGCTAGCACG >sampleID.2 AGCTAGTACG I was think ...
fasta iupac regex perl bash written 9 weeks ago by SaltedPork70 • updated 9 weeks ago by st.ph.n2.2k
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Answer: A: Exception in thread "main" java.io.FileNotFoundException
... Your error is because Trimmomatic cannot find 1R1.fastq. Try providing the full path to this file and check you've got the file name correct. ...
written 9 weeks ago by SaltedPork70
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(Closed) Trim the ID line of a fasta
... I have a fasta file with some very silly ID's (straight from NCBI) that look like this: >KF859747.1 HIV-1 isolate DEURF09UG005 from Uganda gag protein (gag) gene, complete cds; pol protein (pol) gene, partial cds; vif protein (vif), vpr protein (vpr), tat protein (tat), rev protein (rev), v ...
fasta regex written 10 weeks ago by SaltedPork70 • updated 10 weeks ago by lieven.sterck1.1k
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Comment: C: Getting files from BaseMount (Using find command to loop through the symlinks)
... I have also read that BaseMount isn't using symlinks, and yet when I use -L it worked, not sure what's going on there because they look like symlinks to me (in my terminal). ...
written 10 weeks ago by SaltedPork70

Latest awards to SaltedPork

Voter 11 days ago, voted more than 100 times.
Supporter 4 months ago, voted at least 25 times.
Popular Question 16 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

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