User: fire_water

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fire_water70
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4 years, 4 months ago
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Posts by fire_water

<prev • 40 results • page 1 of 4 • next >
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GEO2R Gene Expression
... Hello, I would like to automate the following process that uses GEO2R to analyze gene expression. For each contig I provide, this is the workflow I follow: 0. browse to https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE36545 1. click Profile Graph 2. Enter ID: assembledIsotigs_Contig9526 3. click Set ...
gene written 3 months ago by fire_water70
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Comment: C: Genomestrip 2.0 CNV pipeline
... I'm also experiencing the FunctionEdge error. Did you ever figure out the cause of it? ...
written 6 months ago by fire_water70
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Comment: C: Read Merging Options
... Thanks, genomax. I revised my question title. ...
written 11 months ago by fire_water70
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Read Merging Options
... Hello, I was wondering which software solution everyone is using to merge forward and reverse strands into one strand. [PandaSeq][1] (PAired-eND Assembler for DNA sequences) seems to be one option. Thanks! [1]: https://github.com/neufeld/pandaseq ...
assembly sequence written 11 months ago by fire_water70
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Comment: C: PandaSeq install error: ltld required, install libtool library
... Thanks for the quick reply. In the end, our server administrator installed the following packages which resulted in a successful installation of PANDAseq: libtool-ltdl-2.2.6-15.5.el6.x86_64 libtool-2.2.6-15.5.el6.x86_64 libtool-ltdl-devel-2.2.6-15.5.el6.x86_64 The PANDA is happy now :) ...
written 11 months ago by fire_water70
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PandaSeq install error: ltld required, install libtool library
... Hi, I'm trying to install [PandaSeq][1] as a non-administrator on a Red Hat server but the compiler is returning the following error: ... checking ltdl.h usability... no checking ltdl.h presence... no checking for ltdl.h... no configure: error: *** ltld required, install libtool ...
software error written 11 months ago by fire_water70 • updated 11 months ago by John Marshall1.2k
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(Closed) VCF File: remove certain chromosomes
... I have a few VCF files which contain chromosomes like `GL000207.1` or `NC_007605`. I want to remove all `GL*` and `NC*` chromosomes from the VCF files. Is [VCF-tools][1] capable of doing that or does a better approach exist? Thanks! [1]: https://vcftools.github.io/index.html ...
sequencing written 12 months ago by fire_water70 • updated 12 months ago by Pierre Lindenbaum108k
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GATK: -nct and -nt
... I am trying to understand [GATK's parameters for parallelism][1]: -nt / --num_threads controls the number of data threads sent to the processor -nct / --num_cpu_threads_per_data_thread controls the number of CPU threads allocated to each data thread So, is the following example true? ...
gatk parallel written 14 months ago by fire_water70
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Find Motifs in Genome
... I am wondering if a tool already exists to accomplish the following task... **First, the motifs of interest:** - CATGTG - CATTTG - CACGTG **Second, the pattern to find in the genome:** any motif 6-7nt any motif **Finally, the expected output**: chr, start (of motif), gap (# nt betwe ...
genome written 16 months ago by fire_water70 • updated 16 months ago by shenwei3563.8k
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Comment: C: SAM validation error
... Re-ran `MarkDuplicates` then `BuildBamIndex` using `VALIDATION_STRINGENCY=LENIENT` and the job completed without errors this time! However, a 400 MB log file was created with 2 million lines similar to the following: Ignoring SAM validation error: ERROR: Record 801397832, Read name K00135:24:H3 ...
written 16 months ago by fire_water70

Latest awards to fire_water

Popular Question 6 months ago, created a question with more than 1,000 views. For Mapping Ribosome Profiling Data
Popular Question 6 months ago, created a question with more than 1,000 views. For 3’UTR sequences for Saccharomyces Cerevisiae (yeast)
Popular Question 6 months ago, created a question with more than 1,000 views. For Identify overlapping coordinates
Great Question 11 months ago, created a question with more than 5,000 views. For Seqlogo and Homer
Popular Question 11 months ago, created a question with more than 1,000 views. For Mapping Ribosome Profiling Data
Popular Question 11 months ago, created a question with more than 1,000 views. For 3’UTR sequences for Saccharomyces Cerevisiae (yeast)
Student 2.3 years ago, asked a question with at least 3 up-votes. For Seqlogo and Homer
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Bowtie2 '-P' Threads
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Seqlogo and Homer

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