User: roblogan6

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roblogan620
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Posts by roblogan6

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Comment: C: seqtk illegal option --r, although -r is used in official examples
... I ran this command again: cd seqtk; make And then typed the original command in question using ./seqkt and it worked! Thanks so much for your help. ...
written 6 weeks ago by roblogan620
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Comment: C: seqtk illegal option --r, although -r is used in official examples
... Thank you very much for the response Istvan. Perhaps I don't have it installed correctly? When I am in Users/roblogan/seqtk and run the command I get the following: -bash: seqtk: command not found The contents of the directory are: LICENSE Makefile README.md khash.h kseq.h seqtk.c I have trie ...
written 6 weeks ago by roblogan620
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seqtk illegal option --r, although -r is used in official examples
... Hello, I am trying to get the reverse-complement of an entire fastq file (including symbols). I have used Galaxy for this, but it can be very slow. I came across lh3/seqtk, which advertised as being able to get the reverse complement sequence of a fastq file with the following example from the gith ...
fastq reverse-complement seqtk written 6 weeks ago by roblogan620 • updated 6 weeks ago by Istvan Albert ♦♦ 69k
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Comment: C: How To Convert A Big Fasta File With Multi-Line Dna Sequences Into A Fasta File
... Hi Melendezmatias, I tried your first solution and got the following errors: -bash: unexpected argument `>' to conditional binary operator -bash: syntax error near `>*' Any idea of how to overcome this? Thanks, -Rob ...
written 9 weeks ago by roblogan620
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Comment: C: compare fasta files by sequence
... I get the following error with this: xargs: samtools: No such file or directory. How can I overcome this? Thanks. ...
written 9 weeks ago by roblogan620
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Extracting fastq files, based on their fasta counterparts
... I have two files. One is a multifasta file, then other is a multifastq. The same sequences are found in both files, the files are just in different formats. I have subsets of the multifasta file, and would like to find all those sequences in the multifastq file. The subsets are merely small multifas ...
fasta perl fastq grep database written 9 weeks ago by roblogan620 • updated 9 weeks ago by Brian Bushnell9.0k
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Comment: C: Two multifasta files with the same sequences, but different headers. How to chan
... I couldn't do it locally because grep runs out of memory, but I can run it successfully over the server that I have access to. I need to learn more about grep, awk, sed, etc. They seem quick, powerful, and really simple. Maybe I am deceiving myself about the simple part though! Do you have any resou ...
written 10 weeks ago by roblogan620
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Comment: C: Two multifasta files with the same sequences, but different headers. How to chan
... Thanks! Is there any way to change the grep command to only print out the headers themselves, instead of also including the associated sequences? I am not very familiar with grep. Thanks again. ...
written 12 weeks ago by roblogan620
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Two multifasta files with the same sequences, but different headers. How to change headers to match?
... I have a large multifasta file (about 125,000 sequences) and a smaller multifasta file (about 100 sequences). All sequences in the smaller multifasta file are found in the larger file, but the headers are different. I have many (thousands) of such smaller multifasta files. How can I search the large ...
perl fasta multifasta written 12 weeks ago by roblogan620 • updated 12 weeks ago by shenwei3561.4k
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Visualization of DNA clusters
... I have used DNACLUST to cluster short sequences of DNA. I have all clusters in separate fasta files. I need to visualize the clusters, preferably in neighboring histograms or another commonly used cluster graph output (like what is commonly seen with k-mer "clouds"). The goal is to progressively rel ...
cluster fasta graph dna written 3 months ago by roblogan620

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