User: roblogan6

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roblogan630
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Posts by roblogan6

<prev • 19 results • page 1 of 2 • next >
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Answer: A: Fishing out specific sequences from large PacBio bax.h5 files
... I had sent an email to PacBio technical support about this and got the following response, for those who might be having the same problem: My name is Roberto Lleras, Bioinformatics FAS Manager at PacBio. I'd be happy to answer your question. In order to manually look through the bax.h5 files in or ...
written 4 months ago by roblogan630
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Fishing out specific sequences from large PacBio bax.h5 files
... I have 125,000 individual reads from PacBio in fasta format, processed from bax.h5 files. I have clustered these reads based on unique molecular identifiers. I would now like to align these individual reads per cluster to a reference genome using the PacBio SMRT portal module blasr. I am intereste ...
alignment next-gen blasr pacbio written 4 months ago by roblogan630
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Comment: C: Fastx_reverse_complement error. Invalid quality score even with -Q33
... Thanks Brian for pointing me in the right direction. BBMap worked very well. I noticed you are the author of BBMap too. Very cool! Thanks again. ...
written 4 months ago by roblogan630
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Fastx_reverse_complement error. Invalid quality score even with -Q33
... I am using the fastx toolkit to get the reverse complement of fastq files that are in Sanger phred 33 format. I need to add the -Q33 flag, as discussed in this previous BioStars post https://www.biostars.org/p/86546/ . However, I am getting the following error: fastx_reverse_complement: Error: ...
fastq fastx reverse-complement written 4 months ago by roblogan630
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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 months ago by roblogan630
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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 months ago by roblogan630
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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 months ago by roblogan630 • updated 6 months ago by Istvan Albert ♦♦ 71k
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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 7 months ago by roblogan630
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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 7 months ago by roblogan630
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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 7 months ago by roblogan630 • updated 7 months ago by Brian Bushnell12k

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