User: bird77

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bird7710
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6 days, 4 hours ago
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2 years ago
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j**************@io-warnemuende.de

Posts by bird77

<prev • 28 results • page 1 of 3 • next >
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Convert large protein fasta files to phylip format
... I have run a multiple sequence alignment on a number of concatenated proteins (my input file sizes range from 5 Mb to 100 Mb). But the server from EBI for instance (https://www.ebi.ac.uk/Tools/sfc/emboss_seqret/) limits input size to 2 Mb. Is there a command line tool I can use or a webserver with ...
alignment written 10 days ago by bird7710
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Comment: C: RefSeq ID to TaxID?
... Wonderful, that is exactly what I was looking for. Thank you so much. ...
written 12 weeks ago by bird7710
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Comment: C: BWA error [bns_restore_core] Parse error reading
... If you have spaces in your header, use this instead: ```bash sed -i 's/^[^>]\s*$//g' db/contaminants ``` ...
written 12 weeks ago by bird7710
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Comment: C: RefSeq ID to TaxID?
... ah, wonderful, thank you very much. :-) ...
written 3 months ago by bird7710
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Comment: C: RefSeq ID to TaxID?
... Any idea about this error? ``` $ esearch -db nucleotide -query "NZ_LFWC01000004.1"|esummary|xtract -element TaxId ERROR: No -pattern in command-line arguments ``` xtract seems to cause the error. ...
written 3 months ago by bird7710
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RefSeq ID to TaxID?
... I have a number of RefSeq IDs (like this here NZ_LFWC01000004.1) and I would like to get the tax IDs for the species. Is there a way to automatize that in Bash, Python or R? ...
genome written 3 months ago by bird7710 • updated 3 months ago by Bastien Hervé1.3k
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Assign taxonomy to protein fasta file
... I downloaded a large (50 Mb) protein fasta file from InterPro. It has functional annotation, but I need taxonomical information as well. Is there a tool that can assign taxonomy based on protein sequences? ...
sequence written 3 months ago by bird7710 • updated 3 months ago by Asaf4.8k
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Comment: C: Tool For Taxonomy Classification Of contigs and reads
... Hi Sey, sorry, found the thread much much later. I have protein fasta files which I want to classify. Can you tell me how DIAMOND is used for that? I am not clear about what to use as reference sequence. Thank you. ...
written 3 months ago by bird7710
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Get all completely sequenced genomes from one genus
... Is there an automatic way to get the fasta sequences of all sequenced (preferably completely) genomes within a taxonomic group? And how can I get the taxid for all of these organisms as well? Thank you. ...
genome written 3 months ago by bird7710 • updated 3 months ago by tdmurphy90
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Assembly of 454 raw data (in fastq)
... I need to assemble raw reads from a project that already has been published. The metagenome was sequenced with 454, but the files are only present in fastq format. Is there an assembler which is up-to-date which can assemble long 454 reads with this quality profile? Can UDBA or Megahit deal with t ...
assembly written 4 months ago by bird7710 • updated 3 months ago by colindaven690

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