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  • GenoMax
    replied
    For reference cross-posted: https://www.biostars.org/p/301685/#306693

    Leave a comment:


  • eduillueca
    started a topic Problem with Bowtie 2

    Problem with Bowtie 2

    Hi, I am a student and I'm doing work with data obtained by ChiPSeq. I am trying to do the alignment of the reads with the reference genome, but I get the following error:

    system("./bowtie2-build ./data/tair10.fasta ./data/tair10.fasta") # Indexes reference genome

    ./bowtie2-build: 20: ./bowtie2-build:
    Copyright 2014, Ben Langmead <[email protected]>

    This file is part of Bowtie 2.

    Bowtie 2 is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    Bowtie 2 is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with Bowtie 2. If not, see <http://www.gnu.org/licenses/>.
    : not found
    from: can't read /var/mail/collections
    ./bowtie2-build: 31: ./bowtie2-build: Syntax error: "(" unexpected

    Then, I attempt to put in place the following commands and I get this error:

    > resources <- list(walltime="1:00:00", ntasks=1, ncpus=cores(args), memory="10G")
    > reg <- clusterRun(args, conffile=".BatchJobs.R", template="slurm.tmpl", Njobs=18, runid="01",
    + resourceList=resources)

    Creating dir: /home/usuario/chipseq/results/submitargs01_BJdb_7642
    Saving registry: /home/usuario/chipseq/results/submitargs01_BJdb_7642/registry.RData
    Adding 18 jobs to DB.
    Error in system2(command = command, args = args, stdout = stdout, stderr = stderr, :
    error in running command
    Además: There were 40 warnings (use warnings() to see them)

    > waitForJobs(reg)
    Error in checkRegistry(reg, writeable = FALSE) :
    objeto 'reg' no encontrado

    I don't know where can be the problem. I'm using the tutarial of the following web http://girke.bioinformatics.ucr.edu/...hIPseq_04.html
    for ChIPSeq Analysys. I am working on RStudio with the package systemPipeR

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  • seqadmin
    Multiomics Techniques Advancing Disease Research
    by seqadmin


    New and advanced multiomics tools and technologies have opened new avenues of research and markedly enhanced various disciplines such as disease research and precision medicine1. The practice of merging diverse data from various ‘omes increasingly provides a more holistic understanding of biological systems. As Maddison Masaeli, Co-Founder and CEO at Deepcell, aptly noted, “You can't explain biology in its complex form with one modality.”

    A major leap in the field has
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    02-08-2024, 06:33 AM

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